diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2a5a49de..4e2cf4c1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,8 +2,234 @@
 
 ## Development
 
+### Notes
+
 ### Commits
 
+## v0.2.6
+
+### Notes
+
+1. Put project specific results in seperate repository.
+1. Added 2020 Latvia samples to database, mark as low coverage for now.
+1. Move log directory to within results.
+1. Remove xml tree output from notebooks.
+1. Create scripts to backup, restore, and clean projects.
+1. Remove plot_table rules and script.
+1. Only include visual files into the report.
+1. Put config files inside the associated project directory.
+1. Update function ```identify_local_sample``` to use database.
+1. Environment addition: augur, cartopy, ffpmeg, snp-dists, bokeh.
+1. Create Pairwise SNP matrix.
+1. Remove results folder from docs.
+1. Create new output folder collect for detect snp density.
+1. Remove US Kim strain, mark as laboratory manipulation.
+1. Clean snp density files from version control.
+1. Add country to continent mapping for metadata.
+1. Improvements to plotting missing data and filtering log.
+1. Change all metadata column names to lowercase.
+1. Changed from TreeTime to LSD2.
+1. Included rules to prepare for BEAST.
+1. Jupyter Notebooks pertaining to TreeTime are not used.
+
+### Pull Requests
+
+* [```pull/6```](https://github.com/ktmeaton/plague-phylogeography/pull/6)
+* [```pull/5```](https://github.com/ktmeaton/plague-phylogeography/pull/5)
+
+### Commits
+
+* [```47d7feff```](https://github.com/ktmeaton/plague-phylogeography/commit/47d7feff) Merge pull request #6 from ktmeaton/dev
+* [```4e43f4f6```](https://github.com/ktmeaton/plague-phylogeography/commit/4e43f4f6) update docs notes
+* [```b24b1d97```](https://github.com/ktmeaton/plague-phylogeography/commit/b24b1d97) create newick and nexus trees for beast
+* [```c3097266```](https://github.com/ktmeaton/plague-phylogeography/commit/c3097266) fix branch lengths in conversion scripts
+* [```8fba8a68```](https://github.com/ktmeaton/plague-phylogeography/commit/8fba8a68) add more date col to metadata
+* [```2d5b7545```](https://github.com/ktmeaton/plague-phylogeography/commit/2d5b7545) fix bug in filter_sites
+* [```5dd79f8f```](https://github.com/ktmeaton/plague-phylogeography/commit/5dd79f8f) fix typo in metadata script
+* [```2169f03a```](https://github.com/ktmeaton/plague-phylogeography/commit/2169f03a) add new rule to filter outgroup from iqtree
+* [```f36ae76e```](https://github.com/ktmeaton/plague-phylogeography/commit/f36ae76e) fix typo in eager_tsv script
+* [```62c1c5cf```](https://github.com/ktmeaton/plague-phylogeography/commit/62c1c5cf) remove eager log from output and command
+* [```3790bdd1```](https://github.com/ktmeaton/plague-phylogeography/commit/3790bdd1) first attempt at fixing eager CI
+* [```3acb65fb```](https://github.com/ktmeaton/plague-phylogeography/commit/3acb65fb) restore eager log and fix typo
+* [```cfbc4698```](https://github.com/ktmeaton/plague-phylogeography/commit/cfbc4698) Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
+* [```cd24348d```](https://github.com/ktmeaton/plague-phylogeography/commit/cd24348d) extract and plot subtree
+* [```cd6f133f```](https://github.com/ktmeaton/plague-phylogeography/commit/cd6f133f) catch constant sites in filter script
+* [```035c9292```](https://github.com/ktmeaton/plague-phylogeography/commit/035c9292) renable eager log
+* [```bb0f9ceb```](https://github.com/ktmeaton/plague-phylogeography/commit/bb0f9ceb) first round of plot phylo with compatability for spread3
+* [```4623efb0```](https://github.com/ktmeaton/plague-phylogeography/commit/4623efb0) extra params for lsd2
+* [```35ce0447```](https://github.com/ktmeaton/plague-phylogeography/commit/35ce0447) mega plotting update
+* [```e3b0afce```](https://github.com/ktmeaton/plague-phylogeography/commit/e3b0afce) add timeline to plotting
+* [```7c677023```](https://github.com/ktmeaton/plague-phylogeography/commit/7c677023) add map plotting to notebook
+* [```0cde5c10```](https://github.com/ktmeaton/plague-phylogeography/commit/0cde5c10) remove outgroups in lsd stage
+* [```64c53ba3```](https://github.com/ktmeaton/plague-phylogeography/commit/64c53ba3) switch to lsd2 from source
+* [```cab69592```](https://github.com/ktmeaton/plague-phylogeography/commit/cab69592) print eager output to stdout for troubleshooting
+* [```7361ecdc```](https://github.com/ktmeaton/plague-phylogeography/commit/7361ecdc) possible fix for branch length precision
+* [```cd1b8852```](https://github.com/ktmeaton/plague-phylogeography/commit/cd1b8852) nice rtt plots for prune
+* [```6a5f500e```](https://github.com/ktmeaton/plague-phylogeography/commit/6a5f500e) update pruning and filter to write log
+* [```28af6201```](https://github.com/ktmeaton/plague-phylogeography/commit/28af6201) revert default config to test
+* [```f8e76ad9```](https://github.com/ktmeaton/plague-phylogeography/commit/f8e76ad9) downgrade beast2 to beast1
+* [```058a5cc1```](https://github.com/ktmeaton/plague-phylogeography/commit/058a5cc1) add some fixes to targets
+* [```ad41e99c```](https://github.com/ktmeaton/plague-phylogeography/commit/ad41e99c) implement filtering for each step in phylo
+* [```89280ac1```](https://github.com/ktmeaton/plague-phylogeography/commit/89280ac1) remove constant sites in script prune_alignment
+* [```affe3a53```](https://github.com/ktmeaton/plague-phylogeography/commit/affe3a53) add outgroup metadata and catch in pruning
+* [```ef50cc9f```](https://github.com/ktmeaton/plague-phylogeography/commit/ef50cc9f) filtering alignments for beast
+* [```177b89be```](https://github.com/ktmeaton/plague-phylogeography/commit/177b89be) remove iqtree_scf rule
+* [```70089e28```](https://github.com/ktmeaton/plague-phylogeography/commit/70089e28) tree manipulation and filtering for beast
+* [```4f021720```](https://github.com/ktmeaton/plague-phylogeography/commit/4f021720) add outgroup to database
+* [```d5543d7c```](https://github.com/ktmeaton/plague-phylogeography/commit/d5543d7c) add execut permissions to script
+* [```63d428ca```](https://github.com/ktmeaton/plague-phylogeography/commit/63d428ca) set model in lsd
+* [```2a4df5df```](https://github.com/ktmeaton/plague-phylogeography/commit/2a4df5df) fix targets and scripts typo
+* [```7a9ebd1d```](https://github.com/ktmeaton/plague-phylogeography/commit/7a9ebd1d) update beast prep rule
+* [```1977f379```](https://github.com/ktmeaton/plague-phylogeography/commit/1977f379) stable run for lsd placement
+* [```0dba65c0```](https://github.com/ktmeaton/plague-phylogeography/commit/0dba65c0) prune using branch lengths
+* [```4ab7d149```](https://github.com/ktmeaton/plague-phylogeography/commit/4ab7d149) add alignment pruning to workflow
+* [```992e07fe```](https://github.com/ktmeaton/plague-phylogeography/commit/992e07fe) remove notebooks as target
+* [```01439e7d```](https://github.com/ktmeaton/plague-phylogeography/commit/01439e7d) update placement comments in db
+* [```235a8f6b```](https://github.com/ktmeaton/plague-phylogeography/commit/235a8f6b) remove old project folder
+* [```4312e9cb```](https://github.com/ktmeaton/plague-phylogeography/commit/4312e9cb) add beast conversion info for lsd
+* [```d3e26251```](https://github.com/ktmeaton/plague-phylogeography/commit/d3e26251) test iqtree lsd dating
+* [```602f067e```](https://github.com/ktmeaton/plague-phylogeography/commit/602f067e) upgrade iqtree
+* [```187b5ce6```](https://github.com/ktmeaton/plague-phylogeography/commit/187b5ce6) try better path for trace log
+* [```47130405```](https://github.com/ktmeaton/plague-phylogeography/commit/47130405) add placement comments to db
+* [```c7566fc5```](https://github.com/ktmeaton/plague-phylogeography/commit/c7566fc5) fix clock_plot target typo
+* [```a87ee70d```](https://github.com/ktmeaton/plague-phylogeography/commit/a87ee70d) overhaul directory structure and re-enable jupyter notebooks
+* [```9c4f242c```](https://github.com/ktmeaton/plague-phylogeography/commit/9c4f242c) convert column names to lowercase clocl
+* [```5e061762```](https://github.com/ktmeaton/plague-phylogeography/commit/5e061762) remove checkpoint file
+* [```ef5b7137```](https://github.com/ktmeaton/plague-phylogeography/commit/ef5b7137) start changing column names to lower
+* [```71fa9c39```](https://github.com/ktmeaton/plague-phylogeography/commit/71fa9c39) remove russian samples with no province
+* [```24772de4```](https://github.com/ktmeaton/plague-phylogeography/commit/24772de4) fix jupyter errors in plot missing data
+* [```477462de```](https://github.com/ktmeaton/plague-phylogeography/commit/477462de) update filter sites and plot missing data scripts
+* [```06b960d5```](https://github.com/ktmeaton/plague-phylogeography/commit/06b960d5) remove duplicate record A1122
+* [```9a042e68```](https://github.com/ktmeaton/plague-phylogeography/commit/9a042e68) remove 2med lab strain
+* [```4b1075a5```](https://github.com/ktmeaton/plague-phylogeography/commit/4b1075a5) continue troubleshooting run and beast
+* [```29392806```](https://github.com/ktmeaton/plague-phylogeography/commit/29392806) test projects for geo
+* [```337baaf8```](https://github.com/ktmeaton/plague-phylogeography/commit/337baaf8) Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
+* [```ae2e7017```](https://github.com/ktmeaton/plague-phylogeography/commit/ae2e7017) update notebooks and env
+* [```614327a9```](https://github.com/ktmeaton/plague-phylogeography/commit/614327a9) make diagram slightly narrower
+* [```db616737```](https://github.com/ktmeaton/plague-phylogeography/commit/db616737) fix path coloring for arc diagram
+* [```60222736```](https://github.com/ktmeaton/plague-phylogeography/commit/60222736) more coloring options for arc diagram
+* [```ea703cb7```](https://github.com/ktmeaton/plague-phylogeography/commit/ea703cb7) add continent to metadata
+* [```c13fe426```](https://github.com/ktmeaton/plague-phylogeography/commit/c13fe426) rename arc diagram html
+* [```5ff89fe6```](https://github.com/ktmeaton/plague-phylogeography/commit/5ff89fe6) add javascript code for an arcdiagram
+* [```8bb76cba```](https://github.com/ktmeaton/plague-phylogeography/commit/8bb76cba) save inprogress work optimizing clock
+* [```af6c22fc```](https://github.com/ktmeaton/plague-phylogeography/commit/af6c22fc) remove jupyter targets from all
+* [```207a8927```](https://github.com/ktmeaton/plague-phylogeography/commit/207a8927) finish up clock plot distributions
+* [```6fcaf357```](https://github.com/ktmeaton/plague-phylogeography/commit/6fcaf357) make separate plots for tip date comparison
+* [```00cb9897```](https://github.com/ktmeaton/plague-phylogeography/commit/00cb9897) working on comparing branches
+* [```fd0b0925```](https://github.com/ktmeaton/plague-phylogeography/commit/fd0b0925) generalize the node dating plot
+* [```407c39e0```](https://github.com/ktmeaton/plague-phylogeography/commit/407c39e0) add plotting root marginal distribution to clock plot
+* [```954e6366```](https://github.com/ktmeaton/plague-phylogeography/commit/954e6366) new plotting for marginal date ranges
+* [```4b0ea236```](https://github.com/ktmeaton/plague-phylogeography/commit/4b0ea236) reset project clean config to correct original
+* [```95fd14e1```](https://github.com/ktmeaton/plague-phylogeography/commit/95fd14e1) update clock scripts with better plotting and catch
+* [```f9952c45```](https://github.com/ktmeaton/plague-phylogeography/commit/f9952c45) clean config dir in script
+* [```55c6fb10```](https://github.com/ktmeaton/plague-phylogeography/commit/55c6fb10) dont unload config file
+* [```ecfa6adb```](https://github.com/ktmeaton/plague-phylogeography/commit/ecfa6adb) change rate variation branch to rate rather than multiplier
+* [```ced73b80```](https://github.com/ktmeaton/plague-phylogeography/commit/ced73b80) update project scripts
+* [```790b92bc```](https://github.com/ktmeaton/plague-phylogeography/commit/790b92bc) downgrade beast to 2.6.2
+* [```b79c7fca```](https://github.com/ktmeaton/plague-phylogeography/commit/b79c7fca) add beast and beagle to conda
+* [```1aff367f```](https://github.com/ktmeaton/plague-phylogeography/commit/1aff367f) rename remote json
+* [```e60fcd79```](https://github.com/ktmeaton/plague-phylogeography/commit/e60fcd79) test remote json for modern parse-tree
+* [```bdb6f4ff```](https://github.com/ktmeaton/plague-phylogeography/commit/bdb6f4ff) renable publishing remote auspice
+* [```f7b05225```](https://github.com/ktmeaton/plague-phylogeography/commit/f7b05225) update extract targets
+* [```b9e1f55a```](https://github.com/ktmeaton/plague-phylogeography/commit/b9e1f55a) update filter targets
+* [```5dbe20c4```](https://github.com/ktmeaton/plague-phylogeography/commit/5dbe20c4) remove skyline plot from tracked snakemake output
+* [```77d612a9```](https://github.com/ktmeaton/plague-phylogeography/commit/77d612a9) set simple strict clock as model for testing
+* [```225bd2b0```](https://github.com/ktmeaton/plague-phylogeography/commit/225bd2b0) update script permissions
+* [```4fdb3637```](https://github.com/ktmeaton/plague-phylogeography/commit/4fdb3637) specific configfile param for workflows
+* [```38fbd768```](https://github.com/ktmeaton/plague-phylogeography/commit/38fbd768) backup main project
+* [```644690e7```](https://github.com/ktmeaton/plague-phylogeography/commit/644690e7) cleanup in prep for project migration
+* [```6561bd49```](https://github.com/ktmeaton/plague-phylogeography/commit/6561bd49) update detect snp density collect rule
+* [```0a70215c```](https://github.com/ktmeaton/plague-phylogeography/commit/0a70215c) remove docs-old and outdated report rst
+* [```1604a2ca```](https://github.com/ktmeaton/plague-phylogeography/commit/1604a2ca) remove results folder from docs
+* [```0d1c0896```](https://github.com/ktmeaton/plague-phylogeography/commit/0d1c0896) remove flowdash bio from profiles and update snp matrix
+* [```58a0c2ca```](https://github.com/ktmeaton/plague-phylogeography/commit/58a0c2ca) uninstall and remove lfs
+* [```5ff707ef```](https://github.com/ktmeaton/plague-phylogeography/commit/5ff707ef) switch targets to input
+* [```29c74f49```](https://github.com/ktmeaton/plague-phylogeography/commit/29c74f49) update dev notes
+* [```7f63c196```](https://github.com/ktmeaton/plague-phylogeography/commit/7f63c196) checkpoint before redoing plot aspect
+* [```defe53c9```](https://github.com/ktmeaton/plague-phylogeography/commit/defe53c9) add snp matrix to snakemake
+* [```b1d03b40```](https://github.com/ktmeaton/plague-phylogeography/commit/b1d03b40) plot test snp_matrix
+* [```04167fc6```](https://github.com/ktmeaton/plague-phylogeography/commit/04167fc6) add snp distance to environment
+* [```d45722d8```](https://github.com/ktmeaton/plague-phylogeography/commit/d45722d8) animate branch 0.ANT4
+* [```7109dc0f```](https://github.com/ktmeaton/plague-phylogeography/commit/7109dc0f) animate branch 0.PRE
+* [```c6e5304e```](https://github.com/ktmeaton/plague-phylogeography/commit/c6e5304e) create mp4 spreadmaps with ffmpeg
+* [```28d1f802```](https://github.com/ktmeaton/plague-phylogeography/commit/28d1f802) add animated map of branch 1.PRE
+* [```bad7f301```](https://github.com/ktmeaton/plague-phylogeography/commit/bad7f301) checkpoint before redoing connections
+* [```9b553fab```](https://github.com/ktmeaton/plague-phylogeography/commit/9b553fab) first animation render
+* [```6ad3d6fe```](https://github.com/ktmeaton/plague-phylogeography/commit/6ad3d6fe) arrow checkpoint before animation
+* [```055ccc3b```](https://github.com/ktmeaton/plague-phylogeography/commit/055ccc3b) learned how to use path effects
+* [```9be91012```](https://github.com/ktmeaton/plague-phylogeography/commit/9be91012) working on node connections for geo bias
+* [```f2f159f4```](https://github.com/ktmeaton/plague-phylogeography/commit/f2f159f4) basic work on geo bias
+* [```1d306cb3```](https://github.com/ktmeaton/plague-phylogeography/commit/1d306cb3) ignore locus_coverage_collect directory
+* [```49b37555```](https://github.com/ktmeaton/plague-phylogeography/commit/49b37555) plot locus coverage for all genes on all plasmids
+* [```747744a1```](https://github.com/ktmeaton/plague-phylogeography/commit/747744a1) start plotting tree and heatmap as gridspec
+* [```a19d2800```](https://github.com/ktmeaton/plague-phylogeography/commit/a19d2800) new edits for locus coverage notebook
+* [```53a4208c```](https://github.com/ktmeaton/plague-phylogeography/commit/53a4208c) mark which denmark samples have low coverage
+* [```7b5f05ab```](https://github.com/ktmeaton/plague-phylogeography/commit/7b5f05ab) Merge pull request #5 from ktmeaton/megapestis
+* [```8ec324f5```](https://github.com/ktmeaton/plague-phylogeography/commit/8ec324f5) finish megapestis project mapping
+* [```89cffd37```](https://github.com/ktmeaton/plague-phylogeography/commit/89cffd37) add megapestis non-core bam
+* [```475f3cbc```](https://github.com/ktmeaton/plague-phylogeography/commit/475f3cbc) add noncore to data and database
+* [```e3c4c739```](https://github.com/ktmeaton/plague-phylogeography/commit/e3c4c739) add megapestis ppcp1 bam
+* [```615e3e97```](https://github.com/ktmeaton/plague-phylogeography/commit/615e3e97) convert megapestis pPCP1 to fastq.gz
+* [```a5ba24bf```](https://github.com/ktmeaton/plague-phylogeography/commit/a5ba24bf) adapt locus coverage rule to analyze full genome
+* [```0ec90466```](https://github.com/ktmeaton/plague-phylogeography/commit/0ec90466) ignore megapestis project
+* [```8f0ac25d```](https://github.com/ktmeaton/plague-phylogeography/commit/8f0ac25d) first attempt at plague-phylo full with jupyter snakemake
+* [```c984e13d```](https://github.com/ktmeaton/plague-phylogeography/commit/c984e13d) fix phylogeny indent typo
+* [```d5ee6476```](https://github.com/ktmeaton/plague-phylogeography/commit/d5ee6476) reset large file size again
+* [```a03c9d20```](https://github.com/ktmeaton/plague-phylogeography/commit/a03c9d20) set load to 100 for jupyter notebooks
+* [```154e130b```](https://github.com/ktmeaton/plague-phylogeography/commit/154e130b) add reference data to project main
+* [```ab0355ac```](https://github.com/ktmeaton/plague-phylogeography/commit/ab0355ac) go back to ignoring obj files until testing
+* [```f421e3e2```](https://github.com/ktmeaton/plague-phylogeography/commit/f421e3e2) add parse tree df obj
+* [```ff53f4e9```](https://github.com/ktmeaton/plague-phylogeography/commit/ff53f4e9) add augur to environment
+* [```88edb8aa```](https://github.com/ktmeaton/plague-phylogeography/commit/88edb8aa) add geo to snakemake
+* [```964a5038```](https://github.com/ktmeaton/plague-phylogeography/commit/964a5038) add mugration_model and mugration_plot to snakemake
+* [```99631a55```](https://github.com/ktmeaton/plague-phylogeography/commit/99631a55) remove duplicate record G701
+* [```eec5a21c```](https://github.com/ktmeaton/plague-phylogeography/commit/eec5a21c) fix typo in results_restore
+* [```87cf4259```](https://github.com/ktmeaton/plague-phylogeography/commit/87cf4259) update all target to include clock_plot
+* [```2c98113d```](https://github.com/ktmeaton/plague-phylogeography/commit/2c98113d) add clock plot to test project and report
+* [```36506147```](https://github.com/ktmeaton/plague-phylogeography/commit/36506147) parse_tree and clock_model work for test
+* [```ffcdab91```](https://github.com/ktmeaton/plague-phylogeography/commit/ffcdab91) redo the results backup clean restore scripts
+* [```ac191791```](https://github.com/ktmeaton/plague-phylogeography/commit/ac191791) add project main notebook output
+* [```eece5228```](https://github.com/ktmeaton/plague-phylogeography/commit/eece5228) add project main detection
+* [```a3d51c54```](https://github.com/ktmeaton/plague-phylogeography/commit/a3d51c54) add project main snippy multi
+* [```0ca751ac```](https://github.com/ktmeaton/plague-phylogeography/commit/0ca751ac) Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
+* [```d3d69d8b```](https://github.com/ktmeaton/plague-phylogeography/commit/d3d69d8b) Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
+* [```e0b95892```](https://github.com/ktmeaton/plague-phylogeography/commit/e0b95892) add project main multiqc
+* [```e74e5e92```](https://github.com/ktmeaton/plague-phylogeography/commit/e74e5e92) add project main local metadata
+* [```642e04bd```](https://github.com/ktmeaton/plague-phylogeography/commit/642e04bd) mark Latvia samples as low coverage
+* [```dd418218```](https://github.com/ktmeaton/plague-phylogeography/commit/dd418218) add project main iqtree
+* [```cd84d902```](https://github.com/ktmeaton/plague-phylogeography/commit/cd84d902) add baitsets to megapestis
+* [```1ecd9561```](https://github.com/ktmeaton/plague-phylogeography/commit/1ecd9561) create baitset project megapestis
+* [```47c4c039```](https://github.com/ktmeaton/plague-phylogeography/commit/47c4c039) update metadata and config for project main
+* [```9512900e```](https://github.com/ktmeaton/plague-phylogeography/commit/9512900e) update metadata and config for denmark
+* [```ddccc2fb```](https://github.com/ktmeaton/plague-phylogeography/commit/ddccc2fb) change function identify_local_sample to use database
+* [```7fec05e1```](https://github.com/ktmeaton/plague-phylogeography/commit/7fec05e1) add rsync option to backup results
+* [```2ba19ee7```](https://github.com/ktmeaton/plague-phylogeography/commit/2ba19ee7) remove dummy main data
+* [```9b9a5897```](https://github.com/ktmeaton/plague-phylogeography/commit/9b9a5897) rename main config file
+* [```22eb828b```](https://github.com/ktmeaton/plague-phylogeography/commit/22eb828b) add dummy data for project main
+* [```d368da9b```](https://github.com/ktmeaton/plague-phylogeography/commit/d368da9b) add test metadata
+* [```78c7b943```](https://github.com/ktmeaton/plague-phylogeography/commit/78c7b943) fix rule typos
+* [```645b1855```](https://github.com/ktmeaton/plague-phylogeography/commit/645b1855) add test dir to projects
+* [```1cdbcda9```](https://github.com/ktmeaton/plague-phylogeography/commit/1cdbcda9) remove almost all attached files from report
+* [```e4c16cb8```](https://github.com/ktmeaton/plague-phylogeography/commit/e4c16cb8) add Denmark metadata to db
+* [```95d39c5a```](https://github.com/ktmeaton/plague-phylogeography/commit/95d39c5a) rerun pipeline ci when notebooks change
+* [```f35e391a```](https://github.com/ktmeaton/plague-phylogeography/commit/f35e391a) troubleshoot confidence errors
+* [```f0f1de4a```](https://github.com/ktmeaton/plague-phylogeography/commit/f0f1de4a) remove output files from version control
+* [```ff94ffbf```](https://github.com/ktmeaton/plague-phylogeography/commit/ff94ffbf) add list mode to backup results
+* [```12759227```](https://github.com/ktmeaton/plague-phylogeography/commit/12759227) test remove geo from version control
+* [```2ed37472```](https://github.com/ktmeaton/plague-phylogeography/commit/2ed37472) remove plot_table rules and script
+* [```4be8ca70```](https://github.com/ktmeaton/plague-phylogeography/commit/4be8ca70) remove comments in backup results script
+* [```ff68c7e7```](https://github.com/ktmeaton/plague-phylogeography/commit/ff68c7e7) create new script to backup results
+* [```c61a0ff4```](https://github.com/ktmeaton/plague-phylogeography/commit/c61a0ff4) try to clean results before running CI
+* [```4a532631```](https://github.com/ktmeaton/plague-phylogeography/commit/4a532631) create snakemake rule for clock_model
+* [```03aac6bf```](https://github.com/ktmeaton/plague-phylogeography/commit/03aac6bf) create snakemake rule for parse_tree
+* [```988b47d7```](https://github.com/ktmeaton/plague-phylogeography/commit/988b47d7) add results snippy_multi filter5 aln
+* [```d8265b48```](https://github.com/ktmeaton/plague-phylogeography/commit/d8265b48) remove qualimap results files, too many
+* [```e57f2a02```](https://github.com/ktmeaton/plague-phylogeography/commit/e57f2a02) test add qualimap results
+* [```873d4a48```](https://github.com/ktmeaton/plague-phylogeography/commit/873d4a48) test results upload....
+* [```25421d92```](https://github.com/ktmeaton/plague-phylogeography/commit/25421d92) add 2020 Latvia samples to SRA
+* [```2cd4a7ec```](https://github.com/ktmeaton/plague-phylogeography/commit/2cd4a7ec) add 2020 Latvia samples to database
+* [```ede4ce3b```](https://github.com/ktmeaton/plague-phylogeography/commit/ede4ce3b) Merge pull request #4 from ktmeaton/dev
+
 ## v0.2.5
 
 ### Notes
@@ -22,32 +248,37 @@
 1. Add locus coverage info to nexus tree.
 1. Created spreadmaps for branch major.
 
+### Pull Requests
+
+* [```pull/4```](https://github.com/ktmeaton/plague-phylogeography/pull/4)
+
 ### Commits
 
-* [```3b34108```](https://github.com/ktmeaton/plague-phylogeography/commit/3b34108) add spreadmaps for branch major
-* [```abb53af```](https://github.com/ktmeaton/plague-phylogeography/commit/abb53af) geo spreadmap for branch major
-* [```858b1f9```](https://github.com/ktmeaton/plague-phylogeography/commit/858b1f9) first geo attempt spreadmap for branch number
-* [```5e1ba24```](https://github.com/ktmeaton/plague-phylogeography/commit/5e1ba24) update markdownlint workflow
-* [```3f397c8```](https://github.com/ktmeaton/plague-phylogeography/commit/3f397c8) add cartopy to env
-* [```9c86378```](https://github.com/ktmeaton/plague-phylogeography/commit/9c86378) apply a coverage filter for pPCP1
-* [```8ad86bb```](https://github.com/ktmeaton/plague-phylogeography/commit/8ad86bb) add gene to plasmid depth comparison
-* [```01ecfc0```](https://github.com/ktmeaton/plague-phylogeography/commit/01ecfc0) update locus coverage with depth
-* [```c8bbf55```](https://github.com/ktmeaton/plague-phylogeography/commit/c8bbf55) remove premature exit in locus coverage script
-* [```818d701```](https://github.com/ktmeaton/plague-phylogeography/commit/818d701) run cov and depth on locus coverage
-* [```6868691```](https://github.com/ktmeaton/plague-phylogeography/commit/6868691) make locus coverage it's own notebook
-* [```050dbb4```](https://github.com/ktmeaton/plague-phylogeography/commit/050dbb4) locus coverage including pla
-* [```1bc297b```](https://github.com/ktmeaton/plague-phylogeography/commit/1bc297b) add execute permissions to locus bed
-* [```9efb53a```](https://github.com/ktmeaton/plague-phylogeography/commit/9efb53a) separate rules locus_bed and locus_coverage
-* [```dd3c506```](https://github.com/ktmeaton/plague-phylogeography/commit/dd3c506) Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
-* [```df071bf```](https://github.com/ktmeaton/plague-phylogeography/commit/df071bf) add custom genes to locus coverage
-* [```c3b28e6```](https://github.com/ktmeaton/plague-phylogeography/commit/c3b28e6) Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
-* [```75fbf80```](https://github.com/ktmeaton/plague-phylogeography/commit/75fbf80) add locus coverage results
-* [```cd56bf5```](https://github.com/ktmeaton/plague-phylogeography/commit/cd56bf5) remove output dir from eager rule
-* [```9fc675c```](https://github.com/ktmeaton/plague-phylogeography/commit/9fc675c) add execute permissions to locus_coverage
-* [```d9b0491```](https://github.com/ktmeaton/plague-phylogeography/commit/d9b0491) add rule locus_coverage
-* [```f50c03a```](https://github.com/ktmeaton/plague-phylogeography/commit/f50c03a) separate mugration into model and plot notebooks
-* [```af59396```](https://github.com/ktmeaton/plague-phylogeography/commit/af59396) add report figures and nexus
-* [```9dc027b```](https://github.com/ktmeaton/plague-phylogeography/commit/9dc027b) update badges in README
+* [```596d55c3```](https://github.com/ktmeaton/plague-phylogeography/commit/596d55c3) finish notes for v0.2.5
+* [```3b341089```](https://github.com/ktmeaton/plague-phylogeography/commit/3b341089) add spreadmaps for branch major
+* [```abb53af1```](https://github.com/ktmeaton/plague-phylogeography/commit/abb53af1) geo spreadmap for branch major
+* [```858b1f9e```](https://github.com/ktmeaton/plague-phylogeography/commit/858b1f9e) first geo attempt spreadmap for branch number
+* [```5e1ba24a```](https://github.com/ktmeaton/plague-phylogeography/commit/5e1ba24a) update markdownlint workflow
+* [```3f397c82```](https://github.com/ktmeaton/plague-phylogeography/commit/3f397c82) add cartopy to env
+* [```9c86378f```](https://github.com/ktmeaton/plague-phylogeography/commit/9c86378f) apply a coverage filter for pPCP1
+* [```8ad86bb1```](https://github.com/ktmeaton/plague-phylogeography/commit/8ad86bb1) add gene to plasmid depth comparison
+* [```01ecfc03```](https://github.com/ktmeaton/plague-phylogeography/commit/01ecfc03) update locus coverage with depth
+* [```c8bbf55a```](https://github.com/ktmeaton/plague-phylogeography/commit/c8bbf55a) remove premature exit in locus coverage script
+* [```818d7014```](https://github.com/ktmeaton/plague-phylogeography/commit/818d7014) run cov and depth on locus coverage
+* [```68686914```](https://github.com/ktmeaton/plague-phylogeography/commit/68686914) make locus coverage it's own notebook
+* [```050dbb45```](https://github.com/ktmeaton/plague-phylogeography/commit/050dbb45) locus coverage including pla
+* [```1bc297b5```](https://github.com/ktmeaton/plague-phylogeography/commit/1bc297b5) add execute permissions to locus bed
+* [```9efb53aa```](https://github.com/ktmeaton/plague-phylogeography/commit/9efb53aa) separate rules locus_bed and locus_coverage
+* [```dd3c506a```](https://github.com/ktmeaton/plague-phylogeography/commit/dd3c506a) Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
+* [```df071bf9```](https://github.com/ktmeaton/plague-phylogeography/commit/df071bf9) add custom genes to locus coverage
+* [```c3b28e6f```](https://github.com/ktmeaton/plague-phylogeography/commit/c3b28e6f) Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
+* [```75fbf802```](https://github.com/ktmeaton/plague-phylogeography/commit/75fbf802) add locus coverage results
+* [```cd56bf54```](https://github.com/ktmeaton/plague-phylogeography/commit/cd56bf54) remove output dir from eager rule
+* [```9fc675c3```](https://github.com/ktmeaton/plague-phylogeography/commit/9fc675c3) add execute permissions to locus_coverage
+* [```d9b04913```](https://github.com/ktmeaton/plague-phylogeography/commit/d9b04913) add rule locus_coverage
+* [```f50c03a4```](https://github.com/ktmeaton/plague-phylogeography/commit/f50c03a4) separate mugration into model and plot notebooks
+* [```af59396e```](https://github.com/ktmeaton/plague-phylogeography/commit/af59396e) add report figures and nexus
+* [```9dc027bd```](https://github.com/ktmeaton/plague-phylogeography/commit/9dc027bd) update badges in README
 
 ## v0.2.4
 
@@ -61,14 +292,14 @@
 
 ### Commits
 
-* [```58dd2e1```](https://github.com/ktmeaton/plague-phylogeography/commit/58dd2e1) update notes, changelog, and auspice json for v0.2.4
-* [```46d3d1f```](https://github.com/ktmeaton/plague-phylogeography/commit/46d3d1f) fixed mugration by making sure to copy tree div
-* [```e886d00```](https://github.com/ktmeaton/plague-phylogeography/commit/e886d00) working mugration for Country
-* [```1cdf425```](https://github.com/ktmeaton/plague-phylogeography/commit/1cdf425) working mugration for Branch_Number
-* [```7ea625a```](https://github.com/ktmeaton/plague-phylogeography/commit/7ea625a) save timetrees and divtrees for all relevant methods
-* [```0723ae4```](https://github.com/ktmeaton/plague-phylogeography/commit/0723ae4) update coord_x and coord_y in clock_model
-* [```3d7890e```](https://github.com/ktmeaton/plague-phylogeography/commit/3d7890e) prepare notes for development post-v0.2.3
-* [```4dee9cd```](https://github.com/ktmeaton/plague-phylogeography/commit/4dee9cd) update CHANGELOG for v0.2.3
+* [```58dd2e11```](https://github.com/ktmeaton/plague-phylogeography/commit/58dd2e11) update notes, changelog, and auspice json for v0.2.4
+* [```46d3d1fc```](https://github.com/ktmeaton/plague-phylogeography/commit/46d3d1fc) fixed mugration by making sure to copy tree div
+* [```e886d001```](https://github.com/ktmeaton/plague-phylogeography/commit/e886d001) working mugration for Country
+* [```1cdf4259```](https://github.com/ktmeaton/plague-phylogeography/commit/1cdf4259) working mugration for Branch_Number
+* [```7ea625a6```](https://github.com/ktmeaton/plague-phylogeography/commit/7ea625a6) save timetrees and divtrees for all relevant methods
+* [```0723ae41```](https://github.com/ktmeaton/plague-phylogeography/commit/0723ae41) update coord_x and coord_y in clock_model
+* [```3d7890ee```](https://github.com/ktmeaton/plague-phylogeography/commit/3d7890ee) prepare notes for development post-v0.2.3
+* [```4dee9cd2```](https://github.com/ktmeaton/plague-phylogeography/commit/4dee9cd2) update CHANGELOG for v0.2.3
 
 ## v0.2.3
 
@@ -82,20 +313,20 @@
 
 ### Pull Requests
 
-* [```pull/3```](https://github.com/ktmeaton/plague-phylogeography/pull/3) v0.2.3
+* [```pull/3```](https://github.com/ktmeaton/plague-phylogeography/pull/3)
 
 ### Commits
 
-* [```51adae7```](https://github.com/ktmeaton/plague-phylogeography/commit/51adae7) update notes for v0.2.3
-* [```fc418ff```](https://github.com/ktmeaton/plague-phylogeography/commit/fc418ff) Merge pull request #3 from ktmeaton/dev
-* [```0f8f57d```](https://github.com/ktmeaton/plague-phylogeography/commit/0f8f57d) excellent timetree marginal parameters
-* [```181f944```](https://github.com/ktmeaton/plague-phylogeography/commit/181f944) add comments to nexus for clock_model
-* [```18a7b0e```](https://github.com/ktmeaton/plague-phylogeography/commit/18a7b0e) checkpoint with working but unstable marginal estimate
-* [```ab3f911```](https://github.com/ktmeaton/plague-phylogeography/commit/ab3f911) add comments to nexus for parse_tree
-* [```c33bd64```](https://github.com/ktmeaton/plague-phylogeography/commit/c33bd64) slack:0.1, blm: joint, tc:def, time_marginal:def
-* [```b34519f```](https://github.com/ktmeaton/plague-phylogeography/commit/b34519f) slack:0.5, blm: joint, tc:def, time_marginal:def
-* [```4158f9a```](https://github.com/ktmeaton/plague-phylogeography/commit/4158f9a) first pass at timetree marginal parameters
-* [```1bd0899```](https://github.com/ktmeaton/plague-phylogeography/commit/1bd0899) Merge pull request #2 from ktmeaton/dev
+* [```51adae7d```](https://github.com/ktmeaton/plague-phylogeography/commit/51adae7d) update notes for v0.2.3
+* [```fc418ff6```](https://github.com/ktmeaton/plague-phylogeography/commit/fc418ff6) Merge pull request #3 from ktmeaton/dev
+* [```0f8f57db```](https://github.com/ktmeaton/plague-phylogeography/commit/0f8f57db) excellent timetree marginal parameters
+* [```181f944c```](https://github.com/ktmeaton/plague-phylogeography/commit/181f944c) add comments to nexus for clock_model
+* [```18a7b0e8```](https://github.com/ktmeaton/plague-phylogeography/commit/18a7b0e8) checkpoint with working but unstable marginal estimate
+* [```ab3f9116```](https://github.com/ktmeaton/plague-phylogeography/commit/ab3f9116) add comments to nexus for parse_tree
+* [```c33bd646```](https://github.com/ktmeaton/plague-phylogeography/commit/c33bd646) slack:0.1, blm: joint, tc:def, time_marginal:def
+* [```b34519fb```](https://github.com/ktmeaton/plague-phylogeography/commit/b34519fb) slack:0.5, blm: joint, tc:def, time_marginal:def
+* [```4158f9a4```](https://github.com/ktmeaton/plague-phylogeography/commit/4158f9a4) first pass at timetree marginal parameters
+* [```1bd08990```](https://github.com/ktmeaton/plague-phylogeography/commit/1bd08990) Merge pull request #2 from ktmeaton/dev
 
 ## v0.2.2
 
@@ -118,39 +349,39 @@
 
 ### Pull Requests
 
-* [```pull/2```](https://github.com/ktmeaton/plague-phylogeography/pull/2) v0.2.2
+* [```pull/2```](https://github.com/ktmeaton/plague-phylogeography/pull/2)
 
 ### Commits
 
-* [```be38c62```](https://github.com/ktmeaton/plague-phylogeography/commit/be38c62) use release workflow from autologs
-* [```e5022e1```](https://github.com/ktmeaton/plague-phylogeography/commit/e5022e1) start testing marginal parameters
-* [```c416a43```](https://github.com/ktmeaton/plague-phylogeography/commit/c416a43) rename dev notes to v0.2.2
-* [```bf00b71```](https://github.com/ktmeaton/plague-phylogeography/commit/bf00b71) rerun clock model with good joint param
-* [```6c1d044```](https://github.com/ktmeaton/plague-phylogeography/commit/6c1d044) rerun clock model with terrible param
-* [```8cdab57```](https://github.com/ktmeaton/plague-phylogeography/commit/8cdab57) put jupyter notebook output into results
-* [```e5a74e2```](https://github.com/ktmeaton/plague-phylogeography/commit/e5a74e2) remove old docs parse_tree folder
-* [```1ca7bee```](https://github.com/ktmeaton/plague-phylogeography/commit/1ca7bee) reorder jupyter notebooks
-* [```0b2c710```](https://github.com/ktmeaton/plague-phylogeography/commit/0b2c710) checkpoint before notebook overhaul
-* [```541b953```](https://github.com/ktmeaton/plague-phylogeography/commit/541b953) write tree and df objects with dill for parse_tree
-* [```6a6ccdd```](https://github.com/ktmeaton/plague-phylogeography/commit/6a6ccdd) add dill to environment
-* [```77e2b72```](https://github.com/ktmeaton/plague-phylogeography/commit/77e2b72) add autologs as submodule
-* [```0365b53```](https://github.com/ktmeaton/plague-phylogeography/commit/0365b53) add last timetree model updates
-* [```d211d7f```](https://github.com/ktmeaton/plague-phylogeography/commit/d211d7f) Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
-* [```ff365f7```](https://github.com/ktmeaton/plague-phylogeography/commit/ff365f7) Merge branch 'master' into dev
-* [```ea998f2```](https://github.com/ktmeaton/plague-phylogeography/commit/ea998f2) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```51a4e94```](https://github.com/ktmeaton/plague-phylogeography/commit/51a4e94) checkpoint before using marginal years function
-* [```40b291a```](https://github.com/ktmeaton/plague-phylogeography/commit/40b291a) update docs for v0.2.2
-* [```ff71d89```](https://github.com/ktmeaton/plague-phylogeography/commit/ff71d89) checkpoint before clock modelling in BEAST
-* [```1471e40```](https://github.com/ktmeaton/plague-phylogeography/commit/1471e40) plot tree comparison
-* [```ebeca5e```](https://github.com/ktmeaton/plague-phylogeography/commit/ebeca5e) confirm pruning consistency between tree, dataframe, and alignment.
-* [```ae68969```](https://github.com/ktmeaton/plague-phylogeography/commit/ae68969) prune tree, dataframe, and alignment with treemmer
-* [```667c2f3```](https://github.com/ktmeaton/plague-phylogeography/commit/667c2f3) scatterplot of taxa vs rtl for treemmer
-* [```b66ac4b```](https://github.com/ktmeaton/plague-phylogeography/commit/b66ac4b) disable skyline until gen parameter resolved
-* [```ae63bb4```](https://github.com/ktmeaton/plague-phylogeography/commit/ae63bb4) add clock lengths and model to augur
-* [```85c1712```](https://github.com/ktmeaton/plague-phylogeography/commit/85c1712) add mugration models to augur json
-* [```d5821fc```](https://github.com/ktmeaton/plague-phylogeography/commit/d5821fc) add branch major to auspice config
-* [```504b9cc```](https://github.com/ktmeaton/plague-phylogeography/commit/504b9cc) Begin v0.2.2
-* [```f9b8294```](https://github.com/ktmeaton/plague-phylogeography/commit/f9b8294) add local multiqc to docs
+* [```be38c626```](https://github.com/ktmeaton/plague-phylogeography/commit/be38c626) use release workflow from autologs
+* [```e5022e17```](https://github.com/ktmeaton/plague-phylogeography/commit/e5022e17) start testing marginal parameters
+* [```c416a436```](https://github.com/ktmeaton/plague-phylogeography/commit/c416a436) rename dev notes to v0.2.2
+* [```bf00b71b```](https://github.com/ktmeaton/plague-phylogeography/commit/bf00b71b) rerun clock model with good joint param
+* [```6c1d0446```](https://github.com/ktmeaton/plague-phylogeography/commit/6c1d0446) rerun clock model with terrible param
+* [```8cdab57b```](https://github.com/ktmeaton/plague-phylogeography/commit/8cdab57b) put jupyter notebook output into results
+* [```e5a74e27```](https://github.com/ktmeaton/plague-phylogeography/commit/e5a74e27) remove old docs parse_tree folder
+* [```1ca7beed```](https://github.com/ktmeaton/plague-phylogeography/commit/1ca7beed) reorder jupyter notebooks
+* [```0b2c7103```](https://github.com/ktmeaton/plague-phylogeography/commit/0b2c7103) checkpoint before notebook overhaul
+* [```541b9533```](https://github.com/ktmeaton/plague-phylogeography/commit/541b9533) write tree and df objects with dill for parse_tree
+* [```6a6ccdd6```](https://github.com/ktmeaton/plague-phylogeography/commit/6a6ccdd6) add dill to environment
+* [```77e2b727```](https://github.com/ktmeaton/plague-phylogeography/commit/77e2b727) add autologs as submodule
+* [```0365b53a```](https://github.com/ktmeaton/plague-phylogeography/commit/0365b53a) add last timetree model updates
+* [```d211d7fe```](https://github.com/ktmeaton/plague-phylogeography/commit/d211d7fe) Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
+* [```ff365f78```](https://github.com/ktmeaton/plague-phylogeography/commit/ff365f78) Merge branch 'master' into dev
+* [```ea998f2c```](https://github.com/ktmeaton/plague-phylogeography/commit/ea998f2c) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```51a4e940```](https://github.com/ktmeaton/plague-phylogeography/commit/51a4e940) checkpoint before using marginal years function
+* [```40b291ab```](https://github.com/ktmeaton/plague-phylogeography/commit/40b291ab) update docs for v0.2.2
+* [```ff71d89e```](https://github.com/ktmeaton/plague-phylogeography/commit/ff71d89e) checkpoint before clock modelling in BEAST
+* [```1471e407```](https://github.com/ktmeaton/plague-phylogeography/commit/1471e407) plot tree comparison
+* [```ebeca5e2```](https://github.com/ktmeaton/plague-phylogeography/commit/ebeca5e2) confirm pruning consistency between tree, dataframe, and alignment.
+* [```ae689690```](https://github.com/ktmeaton/plague-phylogeography/commit/ae689690) prune tree, dataframe, and alignment with treemmer
+* [```667c2f3b```](https://github.com/ktmeaton/plague-phylogeography/commit/667c2f3b) scatterplot of taxa vs rtl for treemmer
+* [```b66ac4b5```](https://github.com/ktmeaton/plague-phylogeography/commit/b66ac4b5) disable skyline until gen parameter resolved
+* [```ae63bb45```](https://github.com/ktmeaton/plague-phylogeography/commit/ae63bb45) add clock lengths and model to augur
+* [```85c17124```](https://github.com/ktmeaton/plague-phylogeography/commit/85c17124) add mugration models to augur json
+* [```d5821fc2```](https://github.com/ktmeaton/plague-phylogeography/commit/d5821fc2) add branch major to auspice config
+* [```504b9ccc```](https://github.com/ktmeaton/plague-phylogeography/commit/504b9ccc) Begin v0.2.2
+* [```f9b82946```](https://github.com/ktmeaton/plague-phylogeography/commit/f9b82946) add local multiqc to docs
 
 ## v0.2.1
 
@@ -162,1936 +393,1936 @@
 
 ### Commits
 
-* [```f30964b```](https://github.com/ktmeaton/plague-phylogeography/commit/f30964b) disable singularity from install testing
-* [```4aa4cdc```](https://github.com/ktmeaton/plague-phylogeography/commit/4aa4cdc) release log has truncated commits and changelog has full
-* [```d039c74```](https://github.com/ktmeaton/plague-phylogeography/commit/d039c74) automatically create changelog
-* [```36b672f```](https://github.com/ktmeaton/plague-phylogeography/commit/36b672f) don't run full CI on ver tags
-* [```6d72628```](https://github.com/ktmeaton/plague-phylogeography/commit/6d72628) refine CI workflows to pushes on master or dev
-* [```46e443f```](https://github.com/ktmeaton/plague-phylogeography/commit/46e443f) fix dockerfile path for release
-* [```6aaaa5e```](https://github.com/ktmeaton/plague-phylogeography/commit/6aaaa5e) automate release on ver tags
-* [```ec5504a```](https://github.com/ktmeaton/plague-phylogeography/commit/ec5504a) automate commit notes
-* [```023214c```](https://github.com/ktmeaton/plague-phylogeography/commit/023214c) update notes for v0.2.1
-* [```35ab58c```](https://github.com/ktmeaton/plague-phylogeography/commit/35ab58c) provide config file for flake8 in lint CI
-* [```8857dcc```](https://github.com/ktmeaton/plague-phylogeography/commit/8857dcc) add treemmer notebook results
-* [```f862d44```](https://github.com/ktmeaton/plague-phylogeography/commit/f862d44) disable singularity from CI
-* [```d136168```](https://github.com/ktmeaton/plague-phylogeography/commit/d136168) add treemmer and ete3 to env
-* [```05aa4ce```](https://github.com/ktmeaton/plague-phylogeography/commit/05aa4ce) update workflow for multiqc eager dir
-* [```59e94d4```](https://github.com/ktmeaton/plague-phylogeography/commit/59e94d4) update augur and auspice export for confidence
-* [```9d73947```](https://github.com/ktmeaton/plague-phylogeography/commit/9d73947) separate the augur and auspice json
-* [```730002b```](https://github.com/ktmeaton/plague-phylogeography/commit/730002b) update branch_support notebook and output
-* [```419cbdb```](https://github.com/ktmeaton/plague-phylogeography/commit/419cbdb) update parse_tree notebook and output
-* [```fa522bb```](https://github.com/ktmeaton/plague-phylogeography/commit/fa522bb) auto publish auspice files and use clock filter in parse_tree
-* [```ceffb5f```](https://github.com/ktmeaton/plague-phylogeography/commit/ceffb5f) split timetree into model and plot
-* [```e56adb7```](https://github.com/ktmeaton/plague-phylogeography/commit/e56adb7) split timetree into model and plot
+* [```f30964b8```](https://github.com/ktmeaton/plague-phylogeography/commit/f30964b8) disable singularity from install testing
+* [```4aa4cdca```](https://github.com/ktmeaton/plague-phylogeography/commit/4aa4cdca) release log has truncated commits and changelog has full
+* [```d039c749```](https://github.com/ktmeaton/plague-phylogeography/commit/d039c749) automatically create changelog
+* [```36b672fd```](https://github.com/ktmeaton/plague-phylogeography/commit/36b672fd) don't run full CI on ver tags
+* [```6d726288```](https://github.com/ktmeaton/plague-phylogeography/commit/6d726288) refine CI workflows to pushes on master or dev
+* [```46e443f4```](https://github.com/ktmeaton/plague-phylogeography/commit/46e443f4) fix dockerfile path for release
+* [```6aaaa5e7```](https://github.com/ktmeaton/plague-phylogeography/commit/6aaaa5e7) automate release on ver tags
+* [```ec5504ad```](https://github.com/ktmeaton/plague-phylogeography/commit/ec5504ad) automate commit notes
+* [```023214c8```](https://github.com/ktmeaton/plague-phylogeography/commit/023214c8) update notes for v0.2.1
+* [```35ab58cb```](https://github.com/ktmeaton/plague-phylogeography/commit/35ab58cb) provide config file for flake8 in lint CI
+* [```8857dcc1```](https://github.com/ktmeaton/plague-phylogeography/commit/8857dcc1) add treemmer notebook results
+* [```f862d441```](https://github.com/ktmeaton/plague-phylogeography/commit/f862d441) disable singularity from CI
+* [```d136168a```](https://github.com/ktmeaton/plague-phylogeography/commit/d136168a) add treemmer and ete3 to env
+* [```05aa4ce8```](https://github.com/ktmeaton/plague-phylogeography/commit/05aa4ce8) update workflow for multiqc eager dir
+* [```59e94d4b```](https://github.com/ktmeaton/plague-phylogeography/commit/59e94d4b) update augur and auspice export for confidence
+* [```9d73947a```](https://github.com/ktmeaton/plague-phylogeography/commit/9d73947a) separate the augur and auspice json
+* [```730002b7```](https://github.com/ktmeaton/plague-phylogeography/commit/730002b7) update branch_support notebook and output
+* [```419cbdb8```](https://github.com/ktmeaton/plague-phylogeography/commit/419cbdb8) update parse_tree notebook and output
+* [```fa522bb9```](https://github.com/ktmeaton/plague-phylogeography/commit/fa522bb9) auto publish auspice files and use clock filter in parse_tree
+* [```ceffb5f8```](https://github.com/ktmeaton/plague-phylogeography/commit/ceffb5f8) split timetree into model and plot
+* [```e56adb70```](https://github.com/ktmeaton/plague-phylogeography/commit/e56adb70) split timetree into model and plot
 
 ## v0.2.0
 
 ### Pull Requests
 
-* [```pull/1```](https://github.com/ktmeaton/plague-phylogeography/pull/1) Fully automate dev setup with Gitpod
+* [```pull/1```](https://github.com/ktmeaton/plague-phylogeography/pull/1)
 
 ### Commits
 
-* [```49ec53b```](https://github.com/ktmeaton/plague-phylogeography/commit/49ec53b) update metadata
-* [```18073ac```](https://github.com/ktmeaton/plague-phylogeography/commit/18073ac) update date and geo for lith
-* [```6f9bf01```](https://github.com/ktmeaton/plague-phylogeography/commit/6f9bf01) first post 2020 sample update
-* [```5de74b5```](https://github.com/ktmeaton/plague-phylogeography/commit/5de74b5) docs results cleanup and 2020 phylo
-* [```75821ce```](https://github.com/ktmeaton/plague-phylogeography/commit/75821ce) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
-* [```a8c8e1e```](https://github.com/ktmeaton/plague-phylogeography/commit/a8c8e1e) madd update for 2020 samples
-* [```185e726```](https://github.com/ktmeaton/plague-phylogeography/commit/185e726) update 2020 branch and biovar
-* [```15f143d```](https://github.com/ktmeaton/plague-phylogeography/commit/15f143d) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
-* [```5e0bb64```](https://github.com/ktmeaton/plague-phylogeography/commit/5e0bb64) update all target to include iqtree_scf
-* [```c0638a0```](https://github.com/ktmeaton/plague-phylogeography/commit/c0638a0) add color files creation to parse_tree
-* [```e17e8ac```](https://github.com/ktmeaton/plague-phylogeography/commit/e17e8ac) add Enterobase to study compare
-* [```c1114e4```](https://github.com/ktmeaton/plague-phylogeography/commit/c1114e4) update branch_support with sCF
-* [```1a7eb49```](https://github.com/ktmeaton/plague-phylogeography/commit/1a7eb49) update parse_tree for sCF
-* [```9b6918a```](https://github.com/ktmeaton/plague-phylogeography/commit/9b6918a) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
-* [```2d830a8```](https://github.com/ktmeaton/plague-phylogeography/commit/2d830a8) mark 2020 samples as low cov
-* [```7dfacc8```](https://github.com/ktmeaton/plague-phylogeography/commit/7dfacc8) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
-* [```77327b4```](https://github.com/ktmeaton/plague-phylogeography/commit/77327b4) add latvia samples to db
-* [```7422462```](https://github.com/ktmeaton/plague-phylogeography/commit/7422462) add site concordance factor analysis
-* [```4a4956e```](https://github.com/ktmeaton/plague-phylogeography/commit/4a4956e) notes about sample merging
-* [```295f1ec```](https://github.com/ktmeaton/plague-phylogeography/commit/295f1ec) fix study label
-* [```5cf3021```](https://github.com/ktmeaton/plague-phylogeography/commit/5cf3021) sweep commit for writing
-* [```27390bd```](https://github.com/ktmeaton/plague-phylogeography/commit/27390bd) update study comparison
-* [```39f8e12```](https://github.com/ktmeaton/plague-phylogeography/commit/39f8e12) add bezier to environment
-* [```975aa29```](https://github.com/ktmeaton/plague-phylogeography/commit/975aa29) sanity commit for timetree
-* [```f5035da```](https://github.com/ktmeaton/plague-phylogeography/commit/f5035da) fix timetree extension
-* [```3f89454```](https://github.com/ktmeaton/plague-phylogeography/commit/3f89454) map plotting in timetree
-* [```4cae6a5```](https://github.com/ktmeaton/plague-phylogeography/commit/4cae6a5) update mugration with lat lon
-* [```e7a3102```](https://github.com/ktmeaton/plague-phylogeography/commit/e7a3102) mugration cleanup
-* [```ccc54c5```](https://github.com/ktmeaton/plague-phylogeography/commit/ccc54c5) branch support cleanup
-* [```ff3aae3```](https://github.com/ktmeaton/plague-phylogeography/commit/ff3aae3) parse tree cleanup
-* [```4b16b28```](https://github.com/ktmeaton/plague-phylogeography/commit/4b16b28) plot study comparison
-* [```2552606```](https://github.com/ktmeaton/plague-phylogeography/commit/2552606) new color pal for geo
-* [```c6f860c```](https://github.com/ktmeaton/plague-phylogeography/commit/c6f860c) geo plot now with tree
-* [```8f690a7```](https://github.com/ktmeaton/plague-phylogeography/commit/8f690a7) update parse_tree metadata
-* [```1d59754```](https://github.com/ktmeaton/plague-phylogeography/commit/1d59754) fix bad notebook merge
-* [```b85d5fd```](https://github.com/ktmeaton/plague-phylogeography/commit/b85d5fd) new map and timeline
-* [```d5d8b68```](https://github.com/ktmeaton/plague-phylogeography/commit/d5d8b68) 2020 metadata and plot ancient on world
-* [```726a7b9```](https://github.com/ktmeaton/plague-phylogeography/commit/726a7b9) new metadata for 2020
-* [```9ccb3cd```](https://github.com/ktmeaton/plague-phylogeography/commit/9ccb3cd) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```2c3d537```](https://github.com/ktmeaton/plague-phylogeography/commit/2c3d537) test new method for combining/collapsing records
-* [```e1e97cd```](https://github.com/ktmeaton/plague-phylogeography/commit/e1e97cd) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```d6957a8```](https://github.com/ktmeaton/plague-phylogeography/commit/d6957a8) set pip user in bashrc
-* [```571e32a```](https://github.com/ktmeaton/plague-phylogeography/commit/571e32a) set pip user in bashrc
-* [```87b6681```](https://github.com/ktmeaton/plague-phylogeography/commit/87b6681) fix Ancient SRA comment
-* [```6bf94dc```](https://github.com/ktmeaton/plague-phylogeography/commit/6bf94dc) finish update geo date strain for 2020 biosample
-* [```c6f0633```](https://github.com/ktmeaton/plague-phylogeography/commit/c6f0633) update to 2020 db
-* [```7811f17```](https://github.com/ktmeaton/plague-phylogeography/commit/7811f17) update to 2020 db
-* [```5b77cee```](https://github.com/ktmeaton/plague-phylogeography/commit/5b77cee) updated geo metadata for Sečuán
-* [```2833302```](https://github.com/ktmeaton/plague-phylogeography/commit/2833302) fix geocode for Sečuán province
-* [```3240a09```](https://github.com/ktmeaton/plague-phylogeography/commit/3240a09) add study comparison geo map
-* [```0a7a121```](https://github.com/ktmeaton/plague-phylogeography/commit/0a7a121) add comment and rename metadata file, fix latest config
-* [```e0f678e```](https://github.com/ktmeaton/plague-phylogeography/commit/e0f678e) package lock
-* [```32a1f53```](https://github.com/ktmeaton/plague-phylogeography/commit/32a1f53) suspicious merge
-* [```dd29e92```](https://github.com/ktmeaton/plague-phylogeography/commit/dd29e92) sanity commit before working on heatmap
-* [```f807279```](https://github.com/ktmeaton/plague-phylogeography/commit/f807279) mugration uses config and color_tree
-* [```875800a```](https://github.com/ktmeaton/plague-phylogeography/commit/875800a) branch_support uses config
-* [```44080fa```](https://github.com/ktmeaton/plague-phylogeography/commit/44080fa) parse_tree now uses config
-* [```7652aca```](https://github.com/ktmeaton/plague-phylogeography/commit/7652aca) timetree plots before using config
-* [```16dae92```](https://github.com/ktmeaton/plague-phylogeography/commit/16dae92) mugration standardize ladderize and svg
-* [```0518f6c```](https://github.com/ktmeaton/plague-phylogeography/commit/0518f6c) branch_support standardize ladderize and svg
-* [```270f16e```](https://github.com/ktmeaton/plague-phylogeography/commit/270f16e) parse tree try to standardize ladderize
-* [```27c775b```](https://github.com/ktmeaton/plague-phylogeography/commit/27c775b) svg test for markdown
-* [```3745055```](https://github.com/ktmeaton/plague-phylogeography/commit/3745055) sanity commit of workbooks and output
-* [```aba58c2```](https://github.com/ktmeaton/plague-phylogeography/commit/aba58c2) test mugration auspice
-* [```29e591b```](https://github.com/ktmeaton/plague-phylogeography/commit/29e591b) add latlons to parse tree
-* [```e49af9d```](https://github.com/ktmeaton/plague-phylogeography/commit/e49af9d) test parse tree auspice online
-* [```486127b```](https://github.com/ktmeaton/plague-phylogeography/commit/486127b) make a comprehensive auspice config
-* [```14ba674```](https://github.com/ktmeaton/plague-phylogeography/commit/14ba674) add mugration results to docs
-* [```bfc575a```](https://github.com/ktmeaton/plague-phylogeography/commit/bfc575a) add parse tree results
-* [```cf941a9```](https://github.com/ktmeaton/plague-phylogeography/commit/cf941a9) notebooks export json for auspice
-* [```d17e947```](https://github.com/ktmeaton/plague-phylogeography/commit/d17e947) update branch_support with script name
-* [```7764585```](https://github.com/ktmeaton/plague-phylogeography/commit/7764585) configure npm as root user before installing
-* [```f93ed6f```](https://github.com/ktmeaton/plague-phylogeography/commit/f93ed6f) export json files using dataframe
-* [```7a6b7fe```](https://github.com/ktmeaton/plague-phylogeography/commit/7a6b7fe) add augur to conda env and auspice to dockerfile
-* [```142b7d8```](https://github.com/ktmeaton/plague-phylogeography/commit/142b7d8) fix missing node names and export to json
-* [```c2f86ed```](https://github.com/ktmeaton/plague-phylogeography/commit/c2f86ed) add json python scripts
-* [```d456d4f```](https://github.com/ktmeaton/plague-phylogeography/commit/d456d4f) save subtree outputs before fixing second pandemic fig
-* [```c5ecbe6```](https://github.com/ktmeaton/plague-phylogeography/commit/c5ecbe6) more elegant plotting
-* [```4f3672f```](https://github.com/ktmeaton/plague-phylogeography/commit/4f3672f) add r2 to regression
-* [```de7742b```](https://github.com/ktmeaton/plague-phylogeography/commit/de7742b) divtree timetree comparison
-* [```290e520```](https://github.com/ktmeaton/plague-phylogeography/commit/290e520) nice timetree with nodes and events
-* [```2937112```](https://github.com/ktmeaton/plague-phylogeography/commit/2937112) rename timetree_rtt
-* [```349cf19```](https://github.com/ktmeaton/plague-phylogeography/commit/349cf19) finally working timetree
-* [```581b676```](https://github.com/ktmeaton/plague-phylogeography/commit/581b676) plotting improvements but stats worsen
-* [```78b2144```](https://github.com/ktmeaton/plague-phylogeography/commit/78b2144) start of functional timetree
-* [```26e139e```](https://github.com/ktmeaton/plague-phylogeography/commit/26e139e) successful clock_filter and rtt plot
-* [```db25adf```](https://github.com/ktmeaton/plague-phylogeography/commit/db25adf) trying to figure out root branch length
-* [```2844f03```](https://github.com/ktmeaton/plague-phylogeography/commit/2844f03) add geopandas descartes and contextily
-* [```9d85a2d```](https://github.com/ktmeaton/plague-phylogeography/commit/9d85a2d) remove old large report
-* [```6dd02cb```](https://github.com/ktmeaton/plague-phylogeography/commit/6dd02cb) remove old example folder
-* [```df33c25```](https://github.com/ktmeaton/plague-phylogeography/commit/df33c25) add snippy multi extract report caption
-* [```3439f44```](https://github.com/ktmeaton/plague-phylogeography/commit/3439f44) add a constant sites file for alignment
-* [```0fb9c76```](https://github.com/ktmeaton/plague-phylogeography/commit/0fb9c76) testing of geo mugration and timetree before vcf
-* [```106f77d```](https://github.com/ktmeaton/plague-phylogeography/commit/106f77d) work on contextily tiles
-* [```bc2714e```](https://github.com/ktmeaton/plague-phylogeography/commit/bc2714e) exciting geo progress!
-* [```46cc418```](https://github.com/ktmeaton/plague-phylogeography/commit/46cc418) test geopandas plotting
-* [```4a15bde```](https://github.com/ktmeaton/plague-phylogeography/commit/4a15bde) start geo work
-* [```675862a```](https://github.com/ktmeaton/plague-phylogeography/commit/675862a) plot tips
-* [```500eab3```](https://github.com/ktmeaton/plague-phylogeography/commit/500eab3) plot tree always by div
-* [```ed35165```](https://github.com/ktmeaton/plague-phylogeography/commit/ed35165) better scaling of tree plots
-* [```76eb5c0```](https://github.com/ktmeaton/plague-phylogeography/commit/76eb5c0) use proper pandas df updating with at
-* [```5634b36```](https://github.com/ktmeaton/plague-phylogeography/commit/5634b36) new noteboook results
-* [```c3297e3```](https://github.com/ktmeaton/plague-phylogeography/commit/c3297e3) new result with bam_depth set properly
-* [```1effc29```](https://github.com/ktmeaton/plague-phylogeography/commit/1effc29) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
-* [```4781b14```](https://github.com/ktmeaton/plague-phylogeography/commit/4781b14) add plot het scripts
-* [```1614d9d```](https://github.com/ktmeaton/plague-phylogeography/commit/1614d9d) back up results 2021-01-15
-* [```f440709```](https://github.com/ktmeaton/plague-phylogeography/commit/f440709) mark 2 samples as excess het
-* [```6003795```](https://github.com/ktmeaton/plague-phylogeography/commit/6003795) fix bam depth in snippy pairwise
-* [```65d9de4```](https://github.com/ktmeaton/plague-phylogeography/commit/65d9de4) remove old docs results folders
-* [```a85613d```](https://github.com/ktmeaton/plague-phylogeography/commit/a85613d) upload latest notebooks and results
-* [```7c9f92d```](https://github.com/ktmeaton/plague-phylogeography/commit/7c9f92d) list jupyter notebooks
-* [```a70168a```](https://github.com/ktmeaton/plague-phylogeography/commit/a70168a) update branch support notebook
-* [```4ae1e84```](https://github.com/ktmeaton/plague-phylogeography/commit/4ae1e84) create new notebook and output for branch support
-* [```95d46c8```](https://github.com/ktmeaton/plague-phylogeography/commit/95d46c8) remove other attr from phyloxml parse
-* [```e57f181```](https://github.com/ktmeaton/plague-phylogeography/commit/e57f181) save branch support before change to tree_df
-* [```9384833```](https://github.com/ktmeaton/plague-phylogeography/commit/9384833) remove redundant files that are in report
-* [```37d7c97```](https://github.com/ktmeaton/plague-phylogeography/commit/37d7c97) add latest snippy multi
-* [```a901fe7```](https://github.com/ktmeaton/plague-phylogeography/commit/a901fe7) add latest iqtree
-* [```4ea1cbe```](https://github.com/ktmeaton/plague-phylogeography/commit/4ea1cbe) add latest metadata
-* [```afc06a6```](https://github.com/ktmeaton/plague-phylogeography/commit/afc06a6) add latest multiqc
-* [```a2b3f3a```](https://github.com/ktmeaton/plague-phylogeography/commit/a2b3f3a) more output and plotting for mug
-* [```2bd0b35```](https://github.com/ktmeaton/plague-phylogeography/commit/2bd0b35) mugration notebook to use loops
-* [```4d4876c```](https://github.com/ktmeaton/plague-phylogeography/commit/4d4876c) export branch support tree df
-* [```47902e5```](https://github.com/ktmeaton/plague-phylogeography/commit/47902e5) add branch_support results
-* [```21d8bea```](https://github.com/ktmeaton/plague-phylogeography/commit/21d8bea) remove pyqt and ete3
-* [```636003f```](https://github.com/ktmeaton/plague-phylogeography/commit/636003f) remove pyqt and ete3
-* [```079efca```](https://github.com/ktmeaton/plague-phylogeography/commit/079efca) reset default missing data to 50 for CI
-* [```531abb9```](https://github.com/ktmeaton/plague-phylogeography/commit/531abb9) add plot_missing_data to all target
-* [```37580d6```](https://github.com/ktmeaton/plague-phylogeography/commit/37580d6) make a latest results folder
-* [```24f3a9e```](https://github.com/ktmeaton/plague-phylogeography/commit/24f3a9e) save a production config
-* [```0b36590```](https://github.com/ktmeaton/plague-phylogeography/commit/0b36590) try new targets and all
-* [```4507e7d```](https://github.com/ktmeaton/plague-phylogeography/commit/4507e7d) simplify default snakemake.yaml
-* [```7f767ea```](https://github.com/ktmeaton/plague-phylogeography/commit/7f767ea) experiment with ete3 and pyqt
-* [```a12d58e```](https://github.com/ktmeaton/plague-phylogeography/commit/a12d58e) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```9d79618```](https://github.com/ktmeaton/plague-phylogeography/commit/9d79618) remove duplicate strains
-* [```a002bab```](https://github.com/ktmeaton/plague-phylogeography/commit/a002bab) mugration on branch major
-* [```f118f9a```](https://github.com/ktmeaton/plague-phylogeography/commit/f118f9a) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```001ec7c```](https://github.com/ktmeaton/plague-phylogeography/commit/001ec7c) fix S3 branch
-* [```4024e10```](https://github.com/ktmeaton/plague-phylogeography/commit/4024e10) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```84ea42a```](https://github.com/ktmeaton/plague-phylogeography/commit/84ea42a) last tidy up of branch info
-* [```48db2a1```](https://github.com/ktmeaton/plague-phylogeography/commit/48db2a1) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```bfd1126```](https://github.com/ktmeaton/plague-phylogeography/commit/bfd1126) complete branch annotation
-* [```2237db9```](https://github.com/ktmeaton/plague-phylogeography/commit/2237db9) edit all MED
-* [```18ede7e```](https://github.com/ktmeaton/plague-phylogeography/commit/18ede7e) edit to 2.ANT3
-* [```a2eb6c7```](https://github.com/ktmeaton/plague-phylogeography/commit/a2eb6c7) edit branches Bronze Age 0.PE7 0.PE2 0.PE4
-* [```9ca2361```](https://github.com/ktmeaton/plague-phylogeography/commit/9ca2361) version control black
-* [```f62ff25```](https://github.com/ktmeaton/plague-phylogeography/commit/f62ff25) lint with black v 19
-* [```2c20792```](https://github.com/ktmeaton/plague-phylogeography/commit/2c20792) try to include branch in metadata
-* [```00e1cd5```](https://github.com/ktmeaton/plague-phylogeography/commit/00e1cd5) simplify BioSampleBranch
-* [```435eb65```](https://github.com/ktmeaton/plague-phylogeography/commit/435eb65) finish keller2019 comments
-* [```8231bd0```](https://github.com/ktmeaton/plague-phylogeography/commit/8231bd0) BiosampleBranch Part 11
-* [```47613b3```](https://github.com/ktmeaton/plague-phylogeography/commit/47613b3) BiosampleBranch Part 10
-* [```ccd4997```](https://github.com/ktmeaton/plague-phylogeography/commit/ccd4997) BiosampleBranch Part 9
-* [```32bb5b4```](https://github.com/ktmeaton/plague-phylogeography/commit/32bb5b4) BiosampleBranch Part 8
-* [```5df5a21```](https://github.com/ktmeaton/plague-phylogeography/commit/5df5a21) BiosampleBranch Part 7
-* [```dfe73c4```](https://github.com/ktmeaton/plague-phylogeography/commit/dfe73c4) BiosampleBranch Part 6
-* [```d54dfe9```](https://github.com/ktmeaton/plague-phylogeography/commit/d54dfe9) BiosampleBranch Part 5
-* [```7dfd88a```](https://github.com/ktmeaton/plague-phylogeography/commit/7dfd88a) BiosampleBranch Part 4
-* [```7e414e4```](https://github.com/ktmeaton/plague-phylogeography/commit/7e414e4) BiosampleBranch Part 3
-* [```a1c86f2```](https://github.com/ktmeaton/plague-phylogeography/commit/a1c86f2) disable cartopy for now
-* [```8aa3658```](https://github.com/ktmeaton/plague-phylogeography/commit/8aa3658) BiosampleBranch Part 2
-* [```5e87159```](https://github.com/ktmeaton/plague-phylogeography/commit/5e87159) BiosampleBranch Part 1
-* [```b1b453b```](https://github.com/ktmeaton/plague-phylogeography/commit/b1b453b) add biosample column BioSampleBranch
-* [```52137db```](https://github.com/ktmeaton/plague-phylogeography/commit/52137db) think about cartopy
-* [```e0ad89b```](https://github.com/ktmeaton/plague-phylogeography/commit/e0ad89b) use province for joint plot
-* [```a70dbb8```](https://github.com/ktmeaton/plague-phylogeography/commit/a70dbb8) make kde y more sensitive
-* [```d9cb3db```](https://github.com/ktmeaton/plague-phylogeography/commit/d9cb3db) make kde y more sensitive
-* [```b2f6774```](https://github.com/ktmeaton/plague-phylogeography/commit/b2f6774) make kde y more sensitive
-* [```d7e654b```](https://github.com/ktmeaton/plague-phylogeography/commit/d7e654b) resize joint points
-* [```cb5517e```](https://github.com/ktmeaton/plague-phylogeography/commit/cb5517e) add joint label and kde
-* [```ae8a5f6```](https://github.com/ktmeaton/plague-phylogeography/commit/ae8a5f6) update seaborn for variance bug
-* [```3706627```](https://github.com/ktmeaton/plague-phylogeography/commit/3706627) new analysis with captions
-* [```0a101ce```](https://github.com/ktmeaton/plague-phylogeography/commit/0a101ce) add seaborn plotting
-* [```6812f20```](https://github.com/ktmeaton/plague-phylogeography/commit/6812f20) comprehensive branch support plot
-* [```15c970f```](https://github.com/ktmeaton/plague-phylogeography/commit/15c970f) new legends for confidence
-* [```08ffd22```](https://github.com/ktmeaton/plague-phylogeography/commit/08ffd22) add country histogram
-* [```539cf92```](https://github.com/ktmeaton/plague-phylogeography/commit/539cf92) test country mugration
-* [```dfa23bf```](https://github.com/ktmeaton/plague-phylogeography/commit/dfa23bf) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```58550fe```](https://github.com/ktmeaton/plague-phylogeography/commit/58550fe) update Mongolia foci
-* [```2d2696f```](https://github.com/ktmeaton/plague-phylogeography/commit/2d2696f) run country mugration
-* [```387fa8f```](https://github.com/ktmeaton/plague-phylogeography/commit/387fa8f) improve attr writing to sml
-* [```97955d5```](https://github.com/ktmeaton/plague-phylogeography/commit/97955d5) create jpg instead of png
-* [```ccd4d74```](https://github.com/ktmeaton/plague-phylogeography/commit/ccd4d74) add mugration biovar notebook and output
-* [```d39b36b```](https://github.com/ktmeaton/plague-phylogeography/commit/d39b36b) treetime notebook draft
-* [```7e6db5f```](https://github.com/ktmeaton/plague-phylogeography/commit/7e6db5f) extra pre-commit install step
-* [```9910009```](https://github.com/ktmeaton/plague-phylogeography/commit/9910009) move docs images folder
-* [```f8bd2ac```](https://github.com/ktmeaton/plague-phylogeography/commit/f8bd2ac) Fix get-diff ver typo
-* [```886df5e```](https://github.com/ktmeaton/plague-phylogeography/commit/886df5e) update docker action git diff ver
-* [```809eaa7```](https://github.com/ktmeaton/plague-phylogeography/commit/809eaa7) improve treetime tree parsing and renaming
-* [```87c63db```](https://github.com/ktmeaton/plague-phylogeography/commit/87c63db) fix treetime typo
-* [```f701cae```](https://github.com/ktmeaton/plague-phylogeography/commit/f701cae) update Azerbaijan province
-* [```6613527```](https://github.com/ktmeaton/plague-phylogeography/commit/6613527) update India date
-* [```8f0126b```](https://github.com/ktmeaton/plague-phylogeography/commit/8f0126b) update db with monoglia province fix
-* [```0ec7f33```](https://github.com/ktmeaton/plague-phylogeography/commit/0ec7f33) add treetime to env
-* [```973a0e5```](https://github.com/ktmeaton/plague-phylogeography/commit/973a0e5) better messages for init
-* [```e43e21b```](https://github.com/ktmeaton/plague-phylogeography/commit/e43e21b) better messages for init
-* [```e1bcb96```](https://github.com/ktmeaton/plague-phylogeography/commit/e1bcb96) try line wrap
-* [```05b12af```](https://github.com/ktmeaton/plague-phylogeography/commit/05b12af) try to update gitpod init
-* [```81e8615```](https://github.com/ktmeaton/plague-phylogeography/commit/81e8615) update singularity for action pipeline CI
-* [```8b1432b```](https://github.com/ktmeaton/plague-phylogeography/commit/8b1432b) update singularity action
-* [```efacc2d```](https://github.com/ktmeaton/plague-phylogeography/commit/efacc2d) update miniconda for action pipeline CI
-* [```acc4dfd```](https://github.com/ktmeaton/plague-phylogeography/commit/acc4dfd) update miniconda action
-* [```c27c6e3```](https://github.com/ktmeaton/plague-phylogeography/commit/c27c6e3) try to init pre-commit in gitpod
-* [```90a29b2```](https://github.com/ktmeaton/plague-phylogeography/commit/90a29b2) Update .gitpod.yml
-* [```5606e1b```](https://github.com/ktmeaton/plague-phylogeography/commit/5606e1b) use repo docker image
-* [```0fb62cb```](https://github.com/ktmeaton/plague-phylogeography/commit/0fb62cb) Update .gitpod.yml
-* [```d6c4ed7```](https://github.com/ktmeaton/plague-phylogeography/commit/d6c4ed7) Merge pull request #1 from ktmeaton/ktmeaton/gitpod-setup
-* [```f5a2311```](https://github.com/ktmeaton/plague-phylogeography/commit/f5a2311) Fully automate dev setup with Gitpod
-* [```c0073b4```](https://github.com/ktmeaton/plague-phylogeography/commit/c0073b4) more columns in metadata
-* [```87bf34b```](https://github.com/ktmeaton/plague-phylogeography/commit/87bf34b) consolidate date format
-* [```66d3ce7```](https://github.com/ktmeaton/plague-phylogeography/commit/66d3ce7) fix ancient date format
-* [```1cd4fab```](https://github.com/ktmeaton/plague-phylogeography/commit/1cd4fab) fix ancient date format
-* [```0941b21```](https://github.com/ktmeaton/plague-phylogeography/commit/0941b21) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```3af76c7```](https://github.com/ktmeaton/plague-phylogeography/commit/3af76c7) finish geocoding ancient samples
-* [```ca445d1```](https://github.com/ktmeaton/plague-phylogeography/commit/ca445d1) remove site workflow
-* [```2756d45```](https://github.com/ktmeaton/plague-phylogeography/commit/2756d45) remove old docs workflow
-* [```9a9ef21```](https://github.com/ktmeaton/plague-phylogeography/commit/9a9ef21) detect docker node
-* [```f36534a```](https://github.com/ktmeaton/plague-phylogeography/commit/f36534a) add env IN_DOCKER_CONTAINER to dockerfile
-* [```469b66d```](https://github.com/ktmeaton/plague-phylogeography/commit/469b66d) more ancient annotations
-* [```a740d08```](https://github.com/ktmeaton/plague-phylogeography/commit/a740d08) start geocoding ancient samples
-* [```729d50e```](https://github.com/ktmeaton/plague-phylogeography/commit/729d50e) mark download_sra as a local rule
-* [```42efacc```](https://github.com/ktmeaton/plague-phylogeography/commit/42efacc) update profiles with flowdash bio script
-* [```ed2f521```](https://github.com/ktmeaton/plague-phylogeography/commit/ed2f521) add logic for dry run logging
-* [```eeda3a9```](https://github.com/ktmeaton/plague-phylogeography/commit/eeda3a9) add sql query limit to avoid REMOVE SRA samples
-* [```1ade32f```](https://github.com/ktmeaton/plague-phylogeography/commit/1ade32f) begin comments for SRA Modern
-* [```1cb0f69```](https://github.com/ktmeaton/plague-phylogeography/commit/1cb0f69) add geopy to environment and docs
-* [```b417262```](https://github.com/ktmeaton/plague-phylogeography/commit/b417262) update sra modern comments to TBD
-* [```9a39468```](https://github.com/ktmeaton/plague-phylogeography/commit/9a39468) try add flowdash bio cred at docker runtime
-* [```cd15c18```](https://github.com/ktmeaton/plague-phylogeography/commit/cd15c18) try putting docker flowdash cred in .env file
-* [```9050e9d```](https://github.com/ktmeaton/plague-phylogeography/commit/9050e9d) add flowdash cred to pipeline env
-* [```c20bf1d```](https://github.com/ktmeaton/plague-phylogeography/commit/c20bf1d) better help message for missing token or username
-* [```015270b```](https://github.com/ktmeaton/plague-phylogeography/commit/015270b) add flowdash bio secrets to gh
-* [```8018466```](https://github.com/ktmeaton/plague-phylogeography/commit/8018466) update workflow param for flowdash-bio
-* [```fece7da```](https://github.com/ktmeaton/plague-phylogeography/commit/fece7da) fix target for plot
-* [```a1489fd```](https://github.com/ktmeaton/plague-phylogeography/commit/a1489fd) start work on flowdash-bio logging
-* [```5afa2a5```](https://github.com/ktmeaton/plague-phylogeography/commit/5afa2a5) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```633e9a8```](https://github.com/ktmeaton/plague-phylogeography/commit/633e9a8) start making log script for flowdash-bio
-* [```04187fd```](https://github.com/ktmeaton/plague-phylogeography/commit/04187fd) Create pdf of treefile
-* [```c2a3be4```](https://github.com/ktmeaton/plague-phylogeography/commit/c2a3be4) rearrange and add metadata
-* [```efc513f```](https://github.com/ktmeaton/plague-phylogeography/commit/efc513f) results for 2020-11-09
-* [```d370523```](https://github.com/ktmeaton/plague-phylogeography/commit/d370523) add new snippy log files
-* [```5588d37```](https://github.com/ktmeaton/plague-phylogeography/commit/5588d37) rename docs
-* [```55265b2```](https://github.com/ktmeaton/plague-phylogeography/commit/55265b2) store important results in docs
-* [```6f98324```](https://github.com/ktmeaton/plague-phylogeography/commit/6f98324) change some variants to line rather than scatter
-* [```468aa3b```](https://github.com/ktmeaton/plague-phylogeography/commit/468aa3b) tidy up parsing filtered
-* [```4604fae```](https://github.com/ktmeaton/plague-phylogeography/commit/4604fae) update plotting script
-* [```aa80136```](https://github.com/ktmeaton/plague-phylogeography/commit/aa80136) log passing and failing sites
-* [```fa00709```](https://github.com/ktmeaton/plague-phylogeography/commit/fa00709) allow keeping singletons in script
-* [```47dcd7d```](https://github.com/ktmeaton/plague-phylogeography/commit/47dcd7d) filter singleton sites
-* [```e2f34a8```](https://github.com/ktmeaton/plague-phylogeography/commit/e2f34a8) add logs to report file
-* [```a00d581```](https://github.com/ktmeaton/plague-phylogeography/commit/a00d581) clean up results files now in report
-* [```3b090b8```](https://github.com/ktmeaton/plague-phylogeography/commit/3b090b8) now with multiqc report
-* [```4f9b22c```](https://github.com/ktmeaton/plague-phylogeography/commit/4f9b22c) upgrade nodejs and add nbconvert
-* [```1d39c72```](https://github.com/ktmeaton/plague-phylogeography/commit/1d39c72) second draft phylogeny filtering
-* [```00fc120```](https://github.com/ktmeaton/plague-phylogeography/commit/00fc120) update missing data to have sites in title
-* [```56dcdc4```](https://github.com/ktmeaton/plague-phylogeography/commit/56dcdc4) enable ability to pre-specify iqtree model
-* [```3029ef4```](https://github.com/ktmeaton/plague-phylogeography/commit/3029ef4) enable ability to pre-specify iqtree model
-* [```1f9d14b```](https://github.com/ktmeaton/plague-phylogeography/commit/1f9d14b) run pipelin workflow if config changes
-* [```54be337```](https://github.com/ktmeaton/plague-phylogeography/commit/54be337) restrict sql searches to non-empty cells
-* [```59ab96a```](https://github.com/ktmeaton/plague-phylogeography/commit/59ab96a) finalize assembly comments
-* [```3900055```](https://github.com/ktmeaton/plague-phylogeography/commit/3900055) don't upload logs by default
-* [```afcaf2e```](https://github.com/ktmeaton/plague-phylogeography/commit/afcaf2e) work on phylogeny comments
-* [```6618738```](https://github.com/ktmeaton/plague-phylogeography/commit/6618738) avoid using run rules for report errors
-* [```3902cf1```](https://github.com/ktmeaton/plague-phylogeography/commit/3902cf1) always upload logs, reinstate report for troubleshooting
-* [```34ec827```](https://github.com/ktmeaton/plague-phylogeography/commit/34ec827) test conda pipeline with clean
-* [```cd02a24```](https://github.com/ktmeaton/plague-phylogeography/commit/cd02a24) new metadata remove duplicates
-* [```145b3c5```](https://github.com/ktmeaton/plague-phylogeography/commit/145b3c5) remove duplicates from paths
-* [```2c67caf```](https://github.com/ktmeaton/plague-phylogeography/commit/2c67caf) fix missing _genomic
-* [```f2669cf```](https://github.com/ktmeaton/plague-phylogeography/commit/f2669cf) test metadata automation create
-* [```01d9f46```](https://github.com/ktmeaton/plague-phylogeography/commit/01d9f46) fix script rename
-* [```e876802```](https://github.com/ktmeaton/plague-phylogeography/commit/e876802) fix up all targets
-* [```a00b49e```](https://github.com/ktmeaton/plague-phylogeography/commit/a00b49e) try to fix plot all target
-* [```3305e76```](https://github.com/ktmeaton/plague-phylogeography/commit/3305e76) add metadata to all targets
-* [```54f7c2b```](https://github.com/ktmeaton/plague-phylogeography/commit/54f7c2b) more metadata updates
-* [```84ae661```](https://github.com/ktmeaton/plague-phylogeography/commit/84ae661) rename metadata script
-* [```77920d5```](https://github.com/ktmeaton/plague-phylogeography/commit/77920d5) add metadata creation rule
-* [```74b844f```](https://github.com/ktmeaton/plague-phylogeography/commit/74b844f) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```e9c76ea```](https://github.com/ktmeaton/plague-phylogeography/commit/e9c76ea) better paths for plot missing data
-* [```ed73783```](https://github.com/ktmeaton/plague-phylogeography/commit/ed73783) add missing data plotting to config
-* [```c635630```](https://github.com/ktmeaton/plague-phylogeography/commit/c635630) first draft of phylogeny
-* [```2b354c2```](https://github.com/ktmeaton/plague-phylogeography/commit/2b354c2) test for plotting missing_data
-* [```9a9c300```](https://github.com/ktmeaton/plague-phylogeography/commit/9a9c300) add scripts and env for plotly
-* [```a674d4f```](https://github.com/ktmeaton/plague-phylogeography/commit/a674d4f) improve filtering
-* [```f162c70```](https://github.com/ktmeaton/plague-phylogeography/commit/f162c70) missing data test
-* [```512b962```](https://github.com/ktmeaton/plague-phylogeography/commit/512b962) all multiqc report
-* [```380ede5```](https://github.com/ktmeaton/plague-phylogeography/commit/380ede5) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```dba7e9d```](https://github.com/ktmeaton/plague-phylogeography/commit/dba7e9d) html lint
-* [```41aa8e2```](https://github.com/ktmeaton/plague-phylogeography/commit/41aa8e2) update docs
-* [```e3ac335```](https://github.com/ktmeaton/plague-phylogeography/commit/e3ac335) linting update
-* [```a9cee5d```](https://github.com/ktmeaton/plague-phylogeography/commit/a9cee5d) disable report in pipeline workflow
-* [```cab1400```](https://github.com/ktmeaton/plague-phylogeography/commit/cab1400) filtered multiqc reports
-* [```ae5a1b5```](https://github.com/ktmeaton/plague-phylogeography/commit/ae5a1b5) back up multiqc
-* [```5051adb```](https://github.com/ktmeaton/plague-phylogeography/commit/5051adb) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
-* [```e163bb2```](https://github.com/ktmeaton/plague-phylogeography/commit/e163bb2) update sra report with better param
-* [```0243332```](https://github.com/ktmeaton/plague-phylogeography/commit/0243332) update manual tips
-* [```3f882d0```](https://github.com/ktmeaton/plague-phylogeography/commit/3f882d0) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
-* [```f555330```](https://github.com/ktmeaton/plague-phylogeography/commit/f555330) update manual edits docs
-* [```4808933```](https://github.com/ktmeaton/plague-phylogeography/commit/4808933) add local biosample records
-* [```6401165```](https://github.com/ktmeaton/plague-phylogeography/commit/6401165) finish all comments for sra ancient
-* [```bd1bdfc```](https://github.com/ktmeaton/plague-phylogeography/commit/bd1bdfc) new local report with coverage set to 10
-* [```4d83322```](https://github.com/ktmeaton/plague-phylogeography/commit/4d83322) new local multiqc report with fixed param
-* [```203f226```](https://github.com/ktmeaton/plague-phylogeography/commit/203f226) fix docs typos
-* [```40bd07d```](https://github.com/ktmeaton/plague-phylogeography/commit/40bd07d) docs update
-* [```e525b80```](https://github.com/ktmeaton/plague-phylogeography/commit/e525b80) test new snakemake with report reinstated
-* [```db159f7```](https://github.com/ktmeaton/plague-phylogeography/commit/db159f7) remove cutadapt from env
-* [```553e473```](https://github.com/ktmeaton/plague-phylogeography/commit/553e473) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
-* [```128afeb```](https://github.com/ktmeaton/plague-phylogeography/commit/128afeb) add local multiqc report
-* [```8b54744```](https://github.com/ktmeaton/plague-phylogeography/commit/8b54744) update jupyter notebooks
-* [```44bd273```](https://github.com/ktmeaton/plague-phylogeography/commit/44bd273) add all SRA Ancient comments
-* [```f65dbd5```](https://github.com/ktmeaton/plague-phylogeography/commit/f65dbd5) fix manual edit for GEN72
-* [```948c665```](https://github.com/ktmeaton/plague-phylogeography/commit/948c665) add cutadapt to env for manual edits
-* [```cdf1dd0```](https://github.com/ktmeaton/plague-phylogeography/commit/cdf1dd0) update docs for manual edits
-* [```4ed962d```](https://github.com/ktmeaton/plague-phylogeography/commit/4ed962d) add suffix all to multiqc reports
-* [```7c97478```](https://github.com/ktmeaton/plague-phylogeography/commit/7c97478) add suffix all to multiqc reports
-* [```5ecc8be```](https://github.com/ktmeaton/plague-phylogeography/commit/5ecc8be) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
-* [```09763f4```](https://github.com/ktmeaton/plague-phylogeography/commit/09763f4) add sra multiqc report
-* [```f561274```](https://github.com/ktmeaton/plague-phylogeography/commit/f561274) add ncbimeta to environment
-* [```d305f6d```](https://github.com/ktmeaton/plague-phylogeography/commit/d305f6d) update docs for local and sra
-* [```909ae26```](https://github.com/ktmeaton/plague-phylogeography/commit/909ae26) fix input fastq paths for eager
-* [```ba437a2```](https://github.com/ktmeaton/plague-phylogeography/commit/ba437a2) fix assembly ftp function counting error
-* [```3ee1c5d```](https://github.com/ktmeaton/plague-phylogeography/commit/3ee1c5d) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
-* [```1e9a71a```](https://github.com/ktmeaton/plague-phylogeography/commit/1e9a71a) add assembly multiqc report
-* [```6b8df96```](https://github.com/ktmeaton/plague-phylogeography/commit/6b8df96) update sql commands and parse functions
-* [```6d97a4e```](https://github.com/ktmeaton/plague-phylogeography/commit/6d97a4e) fix typo in download_sra wildcards
-* [```35b0404```](https://github.com/ktmeaton/plague-phylogeography/commit/35b0404) working test of new path system
-* [```0436f1f```](https://github.com/ktmeaton/plague-phylogeography/commit/0436f1f) continue path reconfigure for all option
-* [```e3cb3c7```](https://github.com/ktmeaton/plague-phylogeography/commit/e3cb3c7) start working on new path function system
-* [```f448d23```](https://github.com/ktmeaton/plague-phylogeography/commit/f448d23) working on collect function
-* [```573931c```](https://github.com/ktmeaton/plague-phylogeography/commit/573931c) transition commit from laptop
-* [```4c69d76```](https://github.com/ktmeaton/plague-phylogeography/commit/4c69d76) formally update eager env to 2.2.1
-* [```023efc9```](https://github.com/ktmeaton/plague-phylogeography/commit/023efc9) better sql query
-* [```99aa160```](https://github.com/ktmeaton/plague-phylogeography/commit/99aa160) set default time_min to 6 hours for download_sra
-* [```3765705```](https://github.com/ktmeaton/plague-phylogeography/commit/3765705) remove report functionality until snakemake updated
-* [```3b52517```](https://github.com/ktmeaton/plague-phylogeography/commit/3b52517) actually add docker py test
-* [```14c6313```](https://github.com/ktmeaton/plague-phylogeography/commit/14c6313) also test docker python ver
-* [```e219d7d```](https://github.com/ktmeaton/plague-phylogeography/commit/e219d7d) test python modeule versions
-* [```8c0abb7```](https://github.com/ktmeaton/plague-phylogeography/commit/8c0abb7) change target names from test
-* [```6b8cfda```](https://github.com/ktmeaton/plague-phylogeography/commit/6b8cfda) change sql query and stamp eager to 2.2.1
-* [```a789ab7```](https://github.com/ktmeaton/plague-phylogeography/commit/a789ab7) convert docs from rst to markdown for main
-* [```07b6cf4```](https://github.com/ktmeaton/plague-phylogeography/commit/07b6cf4) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```1a13247```](https://github.com/ktmeaton/plague-phylogeography/commit/1a13247) add new comment structure and remove master tables in db
-* [```e1aa63b```](https://github.com/ktmeaton/plague-phylogeography/commit/e1aa63b) Merge and upload reports
-* [```dfb3f0e```](https://github.com/ktmeaton/plague-phylogeography/commit/dfb3f0e) big run reports and config
-* [```7a99b75```](https://github.com/ktmeaton/plague-phylogeography/commit/7a99b75) use vdb config to prepare for download
-* [```fcd158a```](https://github.com/ktmeaton/plague-phylogeography/commit/fcd158a) add file_acc info to download_sra msg
-* [```d5e7e94```](https://github.com/ktmeaton/plague-phylogeography/commit/d5e7e94) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```1134fda```](https://github.com/ktmeaton/plague-phylogeography/commit/1134fda) eager now ignores qualimap
-* [```4e1e094```](https://github.com/ktmeaton/plague-phylogeography/commit/4e1e094) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```3f0deda```](https://github.com/ktmeaton/plague-phylogeography/commit/3f0deda) update snakemake to 5.26.1 to deal with scheduler issues
-* [```b5c3163```](https://github.com/ktmeaton/plague-phylogeography/commit/b5c3163) remove qualimap from eager
-* [```b428f2f```](https://github.com/ktmeaton/plague-phylogeography/commit/b428f2f) try different eager move strategy
-* [```7c307ea```](https://github.com/ktmeaton/plague-phylogeography/commit/7c307ea) fix snippy multi missing in qualimap
-* [```c8ea5f0```](https://github.com/ktmeaton/plague-phylogeography/commit/c8ea5f0) fix multicore and multimem resources
-* [```b3fad8e```](https://github.com/ktmeaton/plague-phylogeography/commit/b3fad8e) improve multi core processing
-* [```418bdb4```](https://github.com/ktmeaton/plague-phylogeography/commit/418bdb4) user prefetch before fastq-dump
-* [```f8a62c8```](https://github.com/ktmeaton/plague-phylogeography/commit/f8a62c8) update time and script tsv for eager
-* [```303cc52```](https://github.com/ktmeaton/plague-phylogeography/commit/303cc52) bug fix for multiple file sra sample
-* [```09501c3```](https://github.com/ktmeaton/plague-phylogeography/commit/09501c3) mega reprt
-* [```5c192e1```](https://github.com/ktmeaton/plague-phylogeography/commit/5c192e1) update multiqc and set perl locale
-* [```5c5bb1d```](https://github.com/ktmeaton/plague-phylogeography/commit/5c5bb1d) update profiles
-* [```37ff722```](https://github.com/ktmeaton/plague-phylogeography/commit/37ff722) update infoserv profile
-* [```e4f2ea8```](https://github.com/ktmeaton/plague-phylogeography/commit/e4f2ea8) add nextflow log back in
-* [```d3f1f94```](https://github.com/ktmeaton/plague-phylogeography/commit/d3f1f94) add report creation and artifact upload
-* [```25fd12c```](https://github.com/ktmeaton/plague-phylogeography/commit/25fd12c) simplify pipelines to help and all
-* [```c2af37c```](https://github.com/ktmeaton/plague-phylogeography/commit/c2af37c) verbose eager and compute-canada profile update
-* [```a607ec1```](https://github.com/ktmeaton/plague-phylogeography/commit/a607ec1) add docker to pipelin
-* [```50b7318```](https://github.com/ktmeaton/plague-phylogeography/commit/50b7318) remove eager
-* [```a8f4863```](https://github.com/ktmeaton/plague-phylogeography/commit/a8f4863) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```0c60830```](https://github.com/ktmeaton/plague-phylogeography/commit/0c60830) fix typo in Dockerfile
-* [```de726f5```](https://github.com/ktmeaton/plague-phylogeography/commit/de726f5) update docs
-* [```445321b```](https://github.com/ktmeaton/plague-phylogeography/commit/445321b) install ps to dockerfile and run eager as dev
-* [```82babf8```](https://github.com/ktmeaton/plague-phylogeography/commit/82babf8) try to mount volume for docker
-* [```e10a147```](https://github.com/ktmeaton/plague-phylogeography/commit/e10a147) add docker to install test
-* [```a9d717d```](https://github.com/ktmeaton/plague-phylogeography/commit/a9d717d) add eager test
-* [```8f98d7c```](https://github.com/ktmeaton/plague-phylogeography/commit/8f98d7c) remove debugging, configure pipelin
-* [```490e1e3```](https://github.com/ktmeaton/plague-phylogeography/commit/490e1e3) initialize sra-toolkit config file
-* [```787cb51```](https://github.com/ktmeaton/plague-phylogeography/commit/787cb51) rearrange env and add docker authentication
-* [```a8e3ae4```](https://github.com/ktmeaton/plague-phylogeography/commit/a8e3ae4) use different tmate debugger
-* [```38f2e04```](https://github.com/ktmeaton/plague-phylogeography/commit/38f2e04) put debug session at end
-* [```3b99af7```](https://github.com/ktmeaton/plague-phylogeography/commit/3b99af7) disable log handler slack
-* [```32f8e25```](https://github.com/ktmeaton/plague-phylogeography/commit/32f8e25) move debug to help step
-* [```b546ac7```](https://github.com/ktmeaton/plague-phylogeography/commit/b546ac7) add debug session
-* [```eebb472```](https://github.com/ktmeaton/plague-phylogeography/commit/eebb472) see what happens with vdb-config interactive
-* [```742bd13```](https://github.com/ktmeaton/plague-phylogeography/commit/742bd13) update docs
-* [```fc7d0a9```](https://github.com/ktmeaton/plague-phylogeography/commit/fc7d0a9) update after laptop changes
-* [```e5f084d```](https://github.com/ktmeaton/plague-phylogeography/commit/e5f084d) add nf-core eager install
-* [```df2caf8```](https://github.com/ktmeaton/plague-phylogeography/commit/df2caf8) rearrange place of vdb config
-* [```201311d```](https://github.com/ktmeaton/plague-phylogeography/commit/201311d) correct dockerfile path
-* [```10193fe```](https://github.com/ktmeaton/plague-phylogeography/commit/10193fe) try merged conda workflow
-* [```4d7367f```](https://github.com/ktmeaton/plague-phylogeography/commit/4d7367f) try merged conda env
-* [```0ab56c2```](https://github.com/ktmeaton/plague-phylogeography/commit/0ab56c2) test docker file with eager built in
-* [```9f6b251```](https://github.com/ktmeaton/plague-phylogeography/commit/9f6b251) separate into push and release jobs
-* [```03ad8c1```](https://github.com/ktmeaton/plague-phylogeography/commit/03ad8c1) more complicated if check
-* [```bcd723f```](https://github.com/ktmeaton/plague-phylogeography/commit/bcd723f) more complicated if for push
-* [```ca5c63c```](https://github.com/ktmeaton/plague-phylogeography/commit/ca5c63c) test with simple if conditional
-* [```4d0c1d4```](https://github.com/ktmeaton/plague-phylogeography/commit/4d0c1d4) try to use prefix filter
-* [```a496151```](https://github.com/ktmeaton/plague-phylogeography/commit/a496151) exclude docker pipeline
-* [```b521510```](https://github.com/ktmeaton/plague-phylogeography/commit/b521510) change git diff files
-* [```62f01f0```](https://github.com/ktmeaton/plague-phylogeography/commit/62f01f0) add docker back to workflows
-* [```d6d9a0d```](https://github.com/ktmeaton/plague-phylogeography/commit/d6d9a0d) try dockerfile with uuid vdb setup
-* [```626cc16```](https://github.com/ktmeaton/plague-phylogeography/commit/626cc16) add eager to test pipeline
-* [```0314a1c```](https://github.com/ktmeaton/plague-phylogeography/commit/0314a1c) split up and simplify pipelin
-* [```b57b37b```](https://github.com/ktmeaton/plague-phylogeography/commit/b57b37b) dont use special env variable for CONDA
-* [```0a44932```](https://github.com/ktmeaton/plague-phylogeography/commit/0a44932) copy install to pipeline
-* [```da79e2c```](https://github.com/ktmeaton/plague-phylogeography/commit/da79e2c) reset to simple install
-* [```275cb5d```](https://github.com/ktmeaton/plague-phylogeography/commit/275cb5d) test splitting step by matrix
-* [```9f295ec```](https://github.com/ktmeaton/plague-phylogeography/commit/9f295ec) typos in install
-* [```20886e4```](https://github.com/ktmeaton/plague-phylogeography/commit/20886e4) test external env install
-* [```ba5fb7b```](https://github.com/ktmeaton/plague-phylogeography/commit/ba5fb7b) switch back to external container
-* [```ccb4148```](https://github.com/ktmeaton/plague-phylogeography/commit/ccb4148) reset containers for download_sra
-* [```410728d```](https://github.com/ktmeaton/plague-phylogeography/commit/410728d) fix matrix typo
-* [```96f0408```](https://github.com/ktmeaton/plague-phylogeography/commit/96f0408) remove caching
-* [```3e04132```](https://github.com/ktmeaton/plague-phylogeography/commit/3e04132) try to cache conda env
-* [```7c03bd7```](https://github.com/ktmeaton/plague-phylogeography/commit/7c03bd7) fix bash elif typo
-* [```e8ee49a```](https://github.com/ktmeaton/plague-phylogeography/commit/e8ee49a) try pipeline with new org
-* [```4f20468```](https://github.com/ktmeaton/plague-phylogeography/commit/4f20468) make install a matrix again
-* [```4f5da75```](https://github.com/ktmeaton/plague-phylogeography/commit/4f5da75) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```ea8d5ff```](https://github.com/ktmeaton/plague-phylogeography/commit/ea8d5ff) add singularity pull
-* [```f0acb9e```](https://github.com/ktmeaton/plague-phylogeography/commit/f0acb9e) update docs
-* [```378fdf0```](https://github.com/ktmeaton/plague-phylogeography/commit/378fdf0) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```e502b0e```](https://github.com/ktmeaton/plague-phylogeography/commit/e502b0e) add ftputil
-* [```dc6a5c4```](https://github.com/ktmeaton/plague-phylogeography/commit/dc6a5c4) update docs
-* [```17eca57```](https://github.com/ktmeaton/plague-phylogeography/commit/17eca57) move fail fast into strategy
-* [```9d392f3```](https://github.com/ktmeaton/plague-phylogeography/commit/9d392f3) move fail fast into strategy
-* [```c47f072```](https://github.com/ktmeaton/plague-phylogeography/commit/c47f072) install containers
-* [```77bead5```](https://github.com/ktmeaton/plague-phylogeography/commit/77bead5) separate jobs
-* [```7af97c1```](https://github.com/ktmeaton/plague-phylogeography/commit/7af97c1) try conditional with exclude
-* [```7b3ed01```](https://github.com/ktmeaton/plague-phylogeography/commit/7b3ed01) add gfortran
-* [```0ed0394```](https://github.com/ktmeaton/plague-phylogeography/commit/0ed0394) Update install.yaml
-* [```e036d45```](https://github.com/ktmeaton/plague-phylogeography/commit/e036d45) Change matrix if
-* [```ffa7781```](https://github.com/ktmeaton/plague-phylogeography/commit/ffa7781) test minimal install workflow
-* [```82b2438```](https://github.com/ktmeaton/plague-phylogeography/commit/82b2438) test env after qualimap change
-* [```7343171```](https://github.com/ktmeaton/plague-phylogeography/commit/7343171) rename default env
-* [```748af91```](https://github.com/ktmeaton/plague-phylogeography/commit/748af91) rename default env
-* [```1783521```](https://github.com/ktmeaton/plague-phylogeography/commit/1783521) disable plot libs
-* [```359124a```](https://github.com/ktmeaton/plague-phylogeography/commit/359124a) update conda and containers in rules
-* [```3fa270e```](https://github.com/ktmeaton/plague-phylogeography/commit/3fa270e) simplify env
-* [```e966284```](https://github.com/ktmeaton/plague-phylogeography/commit/e966284) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```3d7d828```](https://github.com/ktmeaton/plague-phylogeography/commit/3d7d828) use eager profiles singularity and conda
-* [```2e66be2```](https://github.com/ktmeaton/plague-phylogeography/commit/2e66be2) make nextflow executable
-* [```c2cf147```](https://github.com/ktmeaton/plague-phylogeography/commit/c2cf147) install nextflow
-* [```3c4992e```](https://github.com/ktmeaton/plague-phylogeography/commit/3c4992e) remove singularity defaults
-* [```2bea671```](https://github.com/ktmeaton/plague-phylogeography/commit/2bea671) try to use singularity with eager
-* [```44191f3```](https://github.com/ktmeaton/plague-phylogeography/commit/44191f3) try to use singularity with eager
-* [```4537e93```](https://github.com/ktmeaton/plague-phylogeography/commit/4537e93) fix default env cache
-* [```efd256e```](https://github.com/ktmeaton/plague-phylogeography/commit/efd256e) add containers to all rules
-* [```636db83```](https://github.com/ktmeaton/plague-phylogeography/commit/636db83) try disabling fail fast for matrix jobs
-* [```8149951```](https://github.com/ktmeaton/plague-phylogeography/commit/8149951) change default env name
-* [```2c68b2a```](https://github.com/ktmeaton/plague-phylogeography/commit/2c68b2a) try to label docker images with commit
-* [```fe02ede```](https://github.com/ktmeaton/plague-phylogeography/commit/fe02ede) fix container qc typo
-* [```539c667```](https://github.com/ktmeaton/plague-phylogeography/commit/539c667) give names to envs
-* [```0a900c2```](https://github.com/ktmeaton/plague-phylogeography/commit/0a900c2) change graham to cc with singularity
-* [```c5f6b55```](https://github.com/ktmeaton/plague-phylogeography/commit/c5f6b55) docker prep in workflow
-* [```5f4e055```](https://github.com/ktmeaton/plague-phylogeography/commit/5f4e055) docker and env overhaul
-* [```ab71443```](https://github.com/ktmeaton/plague-phylogeography/commit/ab71443) try build with matrix
-* [```e7ba66a```](https://github.com/ktmeaton/plague-phylogeography/commit/e7ba66a) try build with matrix
-* [```2675f96```](https://github.com/ktmeaton/plague-phylogeography/commit/2675f96) test matrix install
-* [```7c298d2```](https://github.com/ktmeaton/plague-phylogeography/commit/7c298d2) fix typo
-* [```fc250aa```](https://github.com/ktmeaton/plague-phylogeography/commit/fc250aa) test manual push
-* [```3a54612```](https://github.com/ktmeaton/plague-phylogeography/commit/3a54612) specify workdir
-* [```2888e3f```](https://github.com/ktmeaton/plague-phylogeography/commit/2888e3f) make sure conda activates in plot
-* [```85235e1```](https://github.com/ktmeaton/plague-phylogeography/commit/85235e1) make sure conda activates in plot
-* [```60d5044```](https://github.com/ktmeaton/plague-phylogeography/commit/60d5044) try push with gh action
-* [```c1a99b2```](https://github.com/ktmeaton/plague-phylogeography/commit/c1a99b2) try to push to docker hub
-* [```25fe5ce```](https://github.com/ktmeaton/plague-phylogeography/commit/25fe5ce) test run docker plot
-* [```8c8f503```](https://github.com/ktmeaton/plague-phylogeography/commit/8c8f503) test or operator
-* [```c31eb0e```](https://github.com/ktmeaton/plague-phylogeography/commit/c31eb0e) debug output 3
-* [```29f342e```](https://github.com/ktmeaton/plague-phylogeography/commit/29f342e) debug output 2
-* [```471e2f8```](https://github.com/ktmeaton/plague-phylogeography/commit/471e2f8) debug output
-* [```f928177```](https://github.com/ktmeaton/plague-phylogeography/commit/f928177) test contains operator
-* [```c7baccb```](https://github.com/ktmeaton/plague-phylogeography/commit/c7baccb) test contains operator
-* [```7a9d0d4```](https://github.com/ktmeaton/plague-phylogeography/commit/7a9d0d4) test if file change detected
-* [```77f5694```](https://github.com/ktmeaton/plague-phylogeography/commit/77f5694) filter take 2
-* [```245a68b```](https://github.com/ktmeaton/plague-phylogeography/commit/245a68b) try to restrict git diff files
-* [```231c01b```](https://github.com/ktmeaton/plague-phylogeography/commit/231c01b) check for changes before building
-* [```04fdd47```](https://github.com/ktmeaton/plague-phylogeography/commit/04fdd47) check changes test
-* [```5d35fae```](https://github.com/ktmeaton/plague-phylogeography/commit/5d35fae) fix paths in docker workflow
-* [```bfd5ab0```](https://github.com/ktmeaton/plague-phylogeography/commit/bfd5ab0) test docker init
-* [```e7658c4```](https://github.com/ktmeaton/plague-phylogeography/commit/e7658c4) try to fix mamba path
-* [```1af4b97```](https://github.com/ktmeaton/plague-phylogeography/commit/1af4b97) prepare for singularity
-* [```7d05f1b```](https://github.com/ktmeaton/plague-phylogeography/commit/7d05f1b) increase graham profile
-* [```e528393```](https://github.com/ktmeaton/plague-phylogeography/commit/e528393) add all target to testing
-* [```0b8f004```](https://github.com/ktmeaton/plague-phylogeography/commit/0b8f004) fix snippy multi filter target to snps
-* [```36f890e```](https://github.com/ktmeaton/plague-phylogeography/commit/36f890e) automate report upload
-* [```62591f8```](https://github.com/ktmeaton/plague-phylogeography/commit/62591f8) fix multiqc and qualimap dir targets
-* [```dcbffcf```](https://github.com/ktmeaton/plague-phylogeography/commit/dcbffcf) remove assembly print statement
-* [```3039c69```](https://github.com/ktmeaton/plague-phylogeography/commit/3039c69) remove test import
-* [```3ecb83b```](https://github.com/ktmeaton/plague-phylogeography/commit/3ecb83b) add table plot
-* [```f653b0b```](https://github.com/ktmeaton/plague-phylogeography/commit/f653b0b) iqtree and filter with new options
-* [```4c0dabb```](https://github.com/ktmeaton/plague-phylogeography/commit/4c0dabb) fix rstrip and rename local data
-* [```f0ab834```](https://github.com/ktmeaton/plague-phylogeography/commit/f0ab834) fix rstrip and rename local data
-* [```d3687aa```](https://github.com/ktmeaton/plague-phylogeography/commit/d3687aa) fix snippy pairwise wildcards
-* [```11dc463```](https://github.com/ktmeaton/plague-phylogeography/commit/11dc463) reorganize dir structure and troubleshoot eager
-* [```0585c54```](https://github.com/ktmeaton/plague-phylogeography/commit/0585c54) semi-colons
-* [```e30fb38```](https://github.com/ktmeaton/plague-phylogeography/commit/e30fb38) add merge snp density to workflow
-* [```1a7becb```](https://github.com/ktmeaton/plague-phylogeography/commit/1a7becb) fix bed merge input names
-* [```3d0361a```](https://github.com/ktmeaton/plague-phylogeography/commit/3d0361a) add snp density filtering
-* [```fe6d28f```](https://github.com/ktmeaton/plague-phylogeography/commit/fe6d28f) change threads to resources cpus
-* [```70aeeca```](https://github.com/ktmeaton/plague-phylogeography/commit/70aeeca) explictly set some rules to single core, log download_sra
-* [```ca7fbf0```](https://github.com/ktmeaton/plague-phylogeography/commit/ca7fbf0) remove loop from download_sra
-* [```69bc373```](https://github.com/ktmeaton/plague-phylogeography/commit/69bc373) try localrules and cacheing workflow env for pipelin
-* [```5159231```](https://github.com/ktmeaton/plague-phylogeography/commit/5159231) run install with workflow env cache
-* [```b0e9e72```](https://github.com/ktmeaton/plague-phylogeography/commit/b0e9e72) try restricted and parallel eager
-* [```0d7b503```](https://github.com/ktmeaton/plague-phylogeography/commit/0d7b503) add env file creation to install pipeline
-* [```ae41612```](https://github.com/ktmeaton/plague-phylogeography/commit/ae41612) use new conda profile complex
-* [```db61d63```](https://github.com/ktmeaton/plague-phylogeography/commit/db61d63) test new config
-* [```802a06b```](https://github.com/ktmeaton/plague-phylogeography/commit/802a06b) extend time
-* [```d06ade5```](https://github.com/ktmeaton/plague-phylogeography/commit/d06ade5) some fixes for nf-core/eager to avoid offline
-* [```7ad09ed```](https://github.com/ktmeaton/plague-phylogeography/commit/7ad09ed) reset eager channel order
-* [```b4b2fe2```](https://github.com/ktmeaton/plague-phylogeography/commit/b4b2fe2) use a slurm-specific status check script
-* [```e8a45d2```](https://github.com/ktmeaton/plague-phylogeography/commit/e8a45d2) update graham profile
-* [```78869e1```](https://github.com/ktmeaton/plague-phylogeography/commit/78869e1) remove nodes param and try NXF_OPTS
-* [```8a3d9ec```](https://github.com/ktmeaton/plague-phylogeography/commit/8a3d9ec) try to use wildcards.sample for graham log
-* [```a27c829```](https://github.com/ktmeaton/plague-phylogeography/commit/a27c829) update all profiles with generic config, change biosample to sample
-* [```b13fb3d```](https://github.com/ktmeaton/plague-phylogeography/commit/b13fb3d) reorganize config layout
-* [```bfa6786```](https://github.com/ktmeaton/plague-phylogeography/commit/bfa6786) working SLURM profile for graham
-* [```f1196d0```](https://github.com/ktmeaton/plague-phylogeography/commit/f1196d0) switch sbatch param to one line
-* [```dfd0169```](https://github.com/ktmeaton/plague-phylogeography/commit/dfd0169) slurm update after sbatch success
-* [```da8c633```](https://github.com/ktmeaton/plague-phylogeography/commit/da8c633) update slurm permissions
-* [```f5da223```](https://github.com/ktmeaton/plague-phylogeography/commit/f5da223) add slurm status check
-* [```aa7e551```](https://github.com/ktmeaton/plague-phylogeography/commit/aa7e551) remove partition param
-* [```631a3e8```](https://github.com/ktmeaton/plague-phylogeography/commit/631a3e8) hardcode prefix for logs
-* [```19b7934```](https://github.com/ktmeaton/plague-phylogeography/commit/19b7934) fix shadow prefix
-* [```cac3d9a```](https://github.com/ktmeaton/plague-phylogeography/commit/cac3d9a) remove threads config for snippy_pairwise
-* [```e3d971e```](https://github.com/ktmeaton/plague-phylogeography/commit/e3d971e) Merge docs
-* [```1636f8e```](https://github.com/ktmeaton/plague-phylogeography/commit/1636f8e) greater complexity to profiles
-* [```628faa9```](https://github.com/ktmeaton/plague-phylogeography/commit/628faa9) update docs
-* [```85d1661```](https://github.com/ktmeaton/plague-phylogeography/commit/85d1661) add slack test script
-* [```16a4947```](https://github.com/ktmeaton/plague-phylogeography/commit/16a4947) remove conda channel setup
-* [```ac9ad2a```](https://github.com/ktmeaton/plague-phylogeography/commit/ac9ad2a) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```c7a911b```](https://github.com/ktmeaton/plague-phylogeography/commit/c7a911b) make env channels consistent
-* [```a4018e1```](https://github.com/ktmeaton/plague-phylogeography/commit/a4018e1) update docs
-* [```947b1f8```](https://github.com/ktmeaton/plague-phylogeography/commit/947b1f8) Merge remote-tracking branch 'origin/master' into snakemake
-* [```4aa492d```](https://github.com/ktmeaton/plague-phylogeography/commit/4aa492d) add graham profile
-* [```95520ad```](https://github.com/ktmeaton/plague-phylogeography/commit/95520ad) fix bad sra len and report num jobs completed
-* [```88369b3```](https://github.com/ktmeaton/plague-phylogeography/commit/88369b3) remove extra python script, add start jobs log
-* [```0826c37```](https://github.com/ktmeaton/plague-phylogeography/commit/0826c37) try to set timezone
-* [```7cc3f7c```](https://github.com/ktmeaton/plague-phylogeography/commit/7cc3f7c) try slack logging for all rules
-* [```63c50e3```](https://github.com/ktmeaton/plague-phylogeography/commit/63c50e3) add eager to logging
-* [```786e965```](https://github.com/ktmeaton/plague-phylogeography/commit/786e965) test logging of first 2 runs
-* [```448ab66```](https://github.com/ktmeaton/plague-phylogeography/commit/448ab66) better rule logging format
-* [```6e51133```](https://github.com/ktmeaton/plague-phylogeography/commit/6e51133) reinstall bot with chat permissions
-* [```0423d4a```](https://github.com/ktmeaton/plague-phylogeography/commit/0423d4a) try pipeline with new token and bot
-* [```230acbb```](https://github.com/ktmeaton/plague-phylogeography/commit/230acbb) semi colons
-* [```e836f70```](https://github.com/ktmeaton/plague-phylogeography/commit/e836f70) try to limite nf rules to one job concurrently
-* [```2003735```](https://github.com/ktmeaton/plague-phylogeography/commit/2003735) trying download rules with slack logging
-* [```657b855```](https://github.com/ktmeaton/plague-phylogeography/commit/657b855) reset to one-liner
-* [```6a95ee1```](https://github.com/ktmeaton/plague-phylogeography/commit/6a95ee1) try creating .env file in pipeline
-* [```700620e```](https://github.com/ktmeaton/plague-phylogeography/commit/700620e) preparing for slack logging
-* [```67ff70f```](https://github.com/ktmeaton/plague-phylogeography/commit/67ff70f) run snippy multi on all 3 streams
-* [```0b2b493```](https://github.com/ktmeaton/plague-phylogeography/commit/0b2b493) add masking to snippy_multi
-* [```73e2414```](https://github.com/ktmeaton/plague-phylogeography/commit/73e2414) add repeat detection
-* [```be701c8```](https://github.com/ktmeaton/plague-phylogeography/commit/be701c8) sanity commit new scripts
-* [```236c202```](https://github.com/ktmeaton/plague-phylogeography/commit/236c202) restrict infoserv and eager resources
-* [```a2a9fba```](https://github.com/ktmeaton/plague-phylogeography/commit/a2a9fba) never run the update site workflow
-* [```1703ab0```](https://github.com/ktmeaton/plague-phylogeography/commit/1703ab0) test the site action chain
-* [```a8c35db```](https://github.com/ktmeaton/plague-phylogeography/commit/a8c35db) remove site from gitignore
-* [```d4053a2```](https://github.com/ktmeaton/plague-phylogeography/commit/d4053a2) force push new content
-* [```2b7d449```](https://github.com/ktmeaton/plague-phylogeography/commit/2b7d449) try pushing index to gh-pages
-* [```fea299e```](https://github.com/ktmeaton/plague-phylogeography/commit/fea299e) try a different way of adding front matter
-* [```e878b1b```](https://github.com/ktmeaton/plague-phylogeography/commit/e878b1b) test if adding front matter breaks things
-* [```21c76ef```](https://github.com/ktmeaton/plague-phylogeography/commit/21c76ef) test out site building workflow
-* [```f69a2a7```](https://github.com/ktmeaton/plague-phylogeography/commit/f69a2a7) rearrange testing cmd
-* [```a649df2```](https://github.com/ktmeaton/plague-phylogeography/commit/a649df2) limit docs workflow to master
-* [```5b4dd0d```](https://github.com/ktmeaton/plague-phylogeography/commit/5b4dd0d) test docs building again
-* [```14c657b```](https://github.com/ktmeaton/plague-phylogeography/commit/14c657b) limit runtime to 30 min
-* [```d6ab322```](https://github.com/ktmeaton/plague-phylogeography/commit/d6ab322) add link to report html
-* [```2a7a352```](https://github.com/ktmeaton/plague-phylogeography/commit/2a7a352) try to limit threads per rule to 2
-* [```7251a0d```](https://github.com/ktmeaton/plague-phylogeography/commit/7251a0d) simplify snippy multi filtering
-* [```0fb1d24```](https://github.com/ktmeaton/plague-phylogeography/commit/0fb1d24) test out using snp-sites for multi filter
-* [```55efe1a```](https://github.com/ktmeaton/plague-phylogeography/commit/55efe1a) multiqc edits and force log artifact
-* [```e99601f```](https://github.com/ktmeaton/plague-phylogeography/commit/e99601f) add multiqc testing
-* [```0ed39db```](https://github.com/ktmeaton/plague-phylogeography/commit/0ed39db) fix target of test snippy multi filter
-* [```1695db2```](https://github.com/ktmeaton/plague-phylogeography/commit/1695db2) add config file for multiqc
-* [```f714360```](https://github.com/ktmeaton/plague-phylogeography/commit/f714360) add snp-sites to iqtree env and begin qualimap
-* [```0645609```](https://github.com/ktmeaton/plague-phylogeography/commit/0645609) update test pipeline to run snippy_multi_filter separately
-* [```73ddae9```](https://github.com/ktmeaton/plague-phylogeography/commit/73ddae9) update descriptions and ver
-* [```a4668cd```](https://github.com/ktmeaton/plague-phylogeography/commit/a4668cd) add pre-commit to default env
-* [```d2dd968```](https://github.com/ktmeaton/plague-phylogeography/commit/d2dd968) try to use the fconst option
-* [```864a587```](https://github.com/ktmeaton/plague-phylogeography/commit/864a587) fix mixed line endings
-* [```80f7165```](https://github.com/ktmeaton/plague-phylogeography/commit/80f7165) test output snippy_multi_filter
-* [```3891688```](https://github.com/ktmeaton/plague-phylogeography/commit/3891688) fix dup name
-* [```666c82e```](https://github.com/ktmeaton/plague-phylogeography/commit/666c82e) proper max_data settings and new snippy pairwise threads
-* [```a98af3f```](https://github.com/ktmeaton/plague-phylogeography/commit/a98af3f) udpate profiles
-* [```474442b```](https://github.com/ktmeaton/plague-phylogeography/commit/474442b) add graphviz to eager
-* [```9bae116```](https://github.com/ktmeaton/plague-phylogeography/commit/9bae116) split up intensive test rules
-* [```47470f7```](https://github.com/ktmeaton/plague-phylogeography/commit/47470f7) try to limit eager mem
-* [```1d10c3e```](https://github.com/ktmeaton/plague-phylogeography/commit/1d10c3e) disable eager quiet log
-* [```ded90c9```](https://github.com/ktmeaton/plague-phylogeography/commit/ded90c9) rename cache
-* [```ace47f0```](https://github.com/ktmeaton/plague-phylogeography/commit/ace47f0) forgot to put constraints regex in quotes
-* [```09f4a2b```](https://github.com/ktmeaton/plague-phylogeography/commit/09f4a2b) try changing cache key to rebuild cache
-* [```8a189f2```](https://github.com/ktmeaton/plague-phylogeography/commit/8a189f2) further restrict wildcards for reads_origin
-* [```f901e4b```](https://github.com/ktmeaton/plague-phylogeography/commit/f901e4b) restrict ext of download_assembly
-* [```f385d8d```](https://github.com/ktmeaton/plague-phylogeography/commit/f385d8d) test the tsv method separately
-* [```6c97bda```](https://github.com/ktmeaton/plague-phylogeography/commit/6c97bda) add data local with new timestamp
-* [```8f1381f```](https://github.com/ktmeaton/plague-phylogeography/commit/8f1381f) remove bad timestamp data local
-* [```ec5b65a```](https://github.com/ktmeaton/plague-phylogeography/commit/ec5b65a) remove nf from default, reorganize pipeline
-* [```6fde6a7```](https://github.com/ktmeaton/plague-phylogeography/commit/6fde6a7) fix incorrect prefix sra to local
-* [```d5ff7b3```](https://github.com/ktmeaton/plague-phylogeography/commit/d5ff7b3) rearrange the order of download_sra download_assembly
-* [```e891922```](https://github.com/ktmeaton/plague-phylogeography/commit/e891922) new infoserve profile and channels instructions
-* [```db08fc4```](https://github.com/ktmeaton/plague-phylogeography/commit/db08fc4) minor edits to config cmd
-* [```088afe3```](https://github.com/ktmeaton/plague-phylogeography/commit/088afe3) clean up linting and add timeout
-* [```3caee1b```](https://github.com/ktmeaton/plague-phylogeography/commit/3caee1b) major update
-* [```615ea02```](https://github.com/ktmeaton/plague-phylogeography/commit/615ea02) simplify downloading rule
-* [```473f474```](https://github.com/ktmeaton/plague-phylogeography/commit/473f474) sanity commit before rethinking use of import
-* [```b593c7b```](https://github.com/ktmeaton/plague-phylogeography/commit/b593c7b) up to snippy multi with assembly
-* [```ba7ab3f```](https://github.com/ktmeaton/plague-phylogeography/commit/ba7ab3f) rename sqlite_import to sqlite
-* [```6fcee2f```](https://github.com/ktmeaton/plague-phylogeography/commit/6fcee2f) add conda one-liner
-* [```0926ce4```](https://github.com/ktmeaton/plague-phylogeography/commit/0926ce4) back to one-linters
-* [```5ac3fba```](https://github.com/ktmeaton/plague-phylogeography/commit/5ac3fba) back to one-linters
-* [```a80eac2```](https://github.com/ktmeaton/plague-phylogeography/commit/a80eac2) possibly fixed spacing
-* [```e34cd1b```](https://github.com/ktmeaton/plague-phylogeography/commit/e34cd1b) add eager full and download gbff and gff
-* [```b22dabf```](https://github.com/ktmeaton/plague-phylogeography/commit/b22dabf) mark read origin in message
-* [```72cf601```](https://github.com/ktmeaton/plague-phylogeography/commit/72cf601) add the eager_local tsv for testing
-* [```bdecf89```](https://github.com/ktmeaton/plague-phylogeography/commit/bdecf89) add the eager_local tsv for testing
-* [```afe9faf```](https://github.com/ktmeaton/plague-phylogeography/commit/afe9faf) add test_eager_local to test
-* [```ee30530```](https://github.com/ktmeaton/plague-phylogeography/commit/ee30530) Give report cmd a target as help
-* [```fd351cf```](https://github.com/ktmeaton/plague-phylogeography/commit/fd351cf) Add semicolon
-* [```d381380```](https://github.com/ktmeaton/plague-phylogeography/commit/d381380) wrap file input with str for help
-* [```4b6620f```](https://github.com/ktmeaton/plague-phylogeography/commit/4b6620f) remove nextflow pull from install setup
-* [```5843702```](https://github.com/ktmeaton/plague-phylogeography/commit/5843702) cache workflow env and try to install conda env
-* [```7d370a0```](https://github.com/ktmeaton/plague-phylogeography/commit/7d370a0) give eager all available cores
-* [```bc888a8```](https://github.com/ktmeaton/plague-phylogeography/commit/bc888a8) separate nf pull from create
-* [```e8d5b5c```](https://github.com/ktmeaton/plague-phylogeography/commit/e8d5b5c) read nf to eager env
-* [```e0f25c5```](https://github.com/ktmeaton/plague-phylogeography/commit/e0f25c5) forgot semi colons
-* [```ac8a151```](https://github.com/ktmeaton/plague-phylogeography/commit/ac8a151) move nextflow to default env
-* [```6f46ca1```](https://github.com/ktmeaton/plague-phylogeography/commit/6f46ca1) try nextflow with eager
-* [```44aa4d0```](https://github.com/ktmeaton/plague-phylogeography/commit/44aa4d0) try hashing multiple env
-* [```3c0ff5f```](https://github.com/ktmeaton/plague-phylogeography/commit/3c0ff5f) fix nf ver typo
-* [```c4d039c```](https://github.com/ktmeaton/plague-phylogeography/commit/c4d039c) rerun after local data add
-* [```891e68a```](https://github.com/ktmeaton/plague-phylogeography/commit/891e68a) add local testing data
-* [```233e767```](https://github.com/ktmeaton/plague-phylogeography/commit/233e767) add back in eager
-* [```db9b679```](https://github.com/ktmeaton/plague-phylogeography/commit/db9b679) successful file acc implement
-* [```b38088e```](https://github.com/ktmeaton/plague-phylogeography/commit/b38088e) change download dir to data
-* [```3a32865```](https://github.com/ktmeaton/plague-phylogeography/commit/3a32865) start dynamic input for eager
-* [```598d184```](https://github.com/ktmeaton/plague-phylogeography/commit/598d184) add quotes, fix workflow env dir
-* [```658357b```](https://github.com/ktmeaton/plague-phylogeography/commit/658357b) try a new fix in download_sra script for tokens
-* [```dbff3d1```](https://github.com/ktmeaton/plague-phylogeography/commit/dbff3d1) try to fix extra slash in path
-* [```ba22c63```](https://github.com/ktmeaton/plague-phylogeography/commit/ba22c63) fix download ref target
-* [```2c83fbe```](https://github.com/ktmeaton/plague-phylogeography/commit/2c83fbe) fix results_dir for download
-* [```ad7606d```](https://github.com/ktmeaton/plague-phylogeography/commit/ad7606d) add execute permission
-* [```180d8ff```](https://github.com/ktmeaton/plague-phylogeography/commit/180d8ff) add ending semicolons
-* [```cd09afc```](https://github.com/ktmeaton/plague-phylogeography/commit/cd09afc) more path fixes
-* [```69686a0```](https://github.com/ktmeaton/plague-phylogeography/commit/69686a0) more path fixes
-* [```df5bb22```](https://github.com/ktmeaton/plague-phylogeography/commit/df5bb22) fix sqlite db param
-* [```5dfede4```](https://github.com/ktmeaton/plague-phylogeography/commit/5dfede4) trying linting to ignore narratives md
-* [```3745cc8```](https://github.com/ktmeaton/plague-phylogeography/commit/3745cc8) give up on snakemake lint for now
-* [```d3a7bcf```](https://github.com/ktmeaton/plague-phylogeography/commit/d3a7bcf) update custom targets for testing
-* [```4fff30b```](https://github.com/ktmeaton/plague-phylogeography/commit/4fff30b) fix results_dir in alignment
-* [```62f5955```](https://github.com/ktmeaton/plague-phylogeography/commit/62f5955) add in eager to test
-* [```92229f2```](https://github.com/ktmeaton/plague-phylogeography/commit/92229f2) fix results_dir in targets
-* [```69a1343```](https://github.com/ktmeaton/plague-phylogeography/commit/69a1343) separated aggregate targets
-* [```8c96a5a```](https://github.com/ktmeaton/plague-phylogeography/commit/8c96a5a) update for simpler code
-* [```095c72f```](https://github.com/ktmeaton/plague-phylogeography/commit/095c72f) update snakemake to 5.25.0
-* [```2a151ca```](https://github.com/ktmeaton/plague-phylogeography/commit/2a151ca) temp working sra download
-* [```ea64551```](https://github.com/ktmeaton/plague-phylogeography/commit/ea64551) testing sra download
-* [```7f5d29b```](https://github.com/ktmeaton/plague-phylogeography/commit/7f5d29b) reinstate report as new cmd
-* [```0d2171c```](https://github.com/ktmeaton/plague-phylogeography/commit/0d2171c) reinstate report as new cmd
-* [```6ec6f9d```](https://github.com/ktmeaton/plague-phylogeography/commit/6ec6f9d) remove report flag
-* [```2503e21```](https://github.com/ktmeaton/plague-phylogeography/commit/2503e21) fix uses conflict
-* [```427cc01```](https://github.com/ktmeaton/plague-phylogeography/commit/427cc01) lint all
-* [```a49dca8```](https://github.com/ktmeaton/plague-phylogeography/commit/a49dca8) fix the random import
-* [```ea78d60```](https://github.com/ktmeaton/plague-phylogeography/commit/ea78d60) add tree building
-* [```f4e9d11```](https://github.com/ktmeaton/plague-phylogeography/commit/f4e9d11) test new pipeline workflow after updating docs
-* [```04dcd80```](https://github.com/ktmeaton/plague-phylogeography/commit/04dcd80) try run help with conda
-* [```26a6e83```](https://github.com/ktmeaton/plague-phylogeography/commit/26a6e83) update db with master table
-* [```0da9643```](https://github.com/ktmeaton/plague-phylogeography/commit/0da9643) edit desc
-* [```8c6be4e```](https://github.com/ktmeaton/plague-phylogeography/commit/8c6be4e) specify snippy_pairwise cores
-* [```458f45e```](https://github.com/ktmeaton/plague-phylogeography/commit/458f45e) add sqlite db
-* [```ae52abc```](https://github.com/ktmeaton/plague-phylogeography/commit/ae52abc) added gh-actions profile
-* [```6515c4b```](https://github.com/ktmeaton/plague-phylogeography/commit/6515c4b) test for cache hit
-* [```a8e6b72```](https://github.com/ktmeaton/plague-phylogeography/commit/a8e6b72) test for cache hit
-* [```46953e9```](https://github.com/ktmeaton/plague-phylogeography/commit/46953e9) test for cache hit
-* [```a6205bf```](https://github.com/ktmeaton/plague-phylogeography/commit/a6205bf) test help cmd
-* [```827d19a```](https://github.com/ktmeaton/plague-phylogeography/commit/827d19a) fix envs typo
-* [```b2a94f3```](https://github.com/ktmeaton/plague-phylogeography/commit/b2a94f3) use setup conda with mamba
-* [```41cdf8d```](https://github.com/ktmeaton/plague-phylogeography/commit/41cdf8d) test new install workflow
-* [```6cc4a31```](https://github.com/ktmeaton/plague-phylogeography/commit/6cc4a31) add first report
-* [```05185dd```](https://github.com/ktmeaton/plague-phylogeography/commit/05185dd) major nextflow cleanup
-* [```6091832```](https://github.com/ktmeaton/plague-phylogeography/commit/6091832) major nextflow cleanup
-* [```0e2b2e4```](https://github.com/ktmeaton/plague-phylogeography/commit/0e2b2e4) added report functionality
-* [```0ac0668```](https://github.com/ktmeaton/plague-phylogeography/commit/0ac0668) consolidate sample id
-* [```054e10e```](https://github.com/ktmeaton/plague-phylogeography/commit/054e10e) put func in sep file, figured out variable input
-* [```135b298```](https://github.com/ktmeaton/plague-phylogeography/commit/135b298) fix all target, now reads from db
-* [```68eb2d7```](https://github.com/ktmeaton/plague-phylogeography/commit/68eb2d7) figuring out the chain
-* [```7a7c1f9```](https://github.com/ktmeaton/plague-phylogeography/commit/7a7c1f9) reorganize in workflow dir
-* [```30318da```](https://github.com/ktmeaton/plague-phylogeography/commit/30318da) separated sqlite and download rules
-* [```6ac0dd7```](https://github.com/ktmeaton/plague-phylogeography/commit/6ac0dd7) smoothed out a downloading option
-* [```133033b```](https://github.com/ktmeaton/plague-phylogeography/commit/133033b) more snakemake testing
-* [```ddb90cf```](https://github.com/ktmeaton/plague-phylogeography/commit/ddb90cf) update docs
-* [```6d0168e```](https://github.com/ktmeaton/plague-phylogeography/commit/6d0168e) create rules for local reads and eager
-* [```eae2213```](https://github.com/ktmeaton/plague-phylogeography/commit/eae2213) first changes with snakemake
+* [```49ec53bd```](https://github.com/ktmeaton/plague-phylogeography/commit/49ec53bd) update metadata
+* [```18073acd```](https://github.com/ktmeaton/plague-phylogeography/commit/18073acd) update date and geo for lith
+* [```6f9bf01e```](https://github.com/ktmeaton/plague-phylogeography/commit/6f9bf01e) first post 2020 sample update
+* [```5de74b58```](https://github.com/ktmeaton/plague-phylogeography/commit/5de74b58) docs results cleanup and 2020 phylo
+* [```75821ce1```](https://github.com/ktmeaton/plague-phylogeography/commit/75821ce1) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
+* [```a8c8e1ef```](https://github.com/ktmeaton/plague-phylogeography/commit/a8c8e1ef) madd update for 2020 samples
+* [```185e726d```](https://github.com/ktmeaton/plague-phylogeography/commit/185e726d) update 2020 branch and biovar
+* [```15f143d2```](https://github.com/ktmeaton/plague-phylogeography/commit/15f143d2) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
+* [```5e0bb642```](https://github.com/ktmeaton/plague-phylogeography/commit/5e0bb642) update all target to include iqtree_scf
+* [```c0638a06```](https://github.com/ktmeaton/plague-phylogeography/commit/c0638a06) add color files creation to parse_tree
+* [```e17e8aca```](https://github.com/ktmeaton/plague-phylogeography/commit/e17e8aca) add Enterobase to study compare
+* [```c1114e45```](https://github.com/ktmeaton/plague-phylogeography/commit/c1114e45) update branch_support with sCF
+* [```1a7eb49e```](https://github.com/ktmeaton/plague-phylogeography/commit/1a7eb49e) update parse_tree for sCF
+* [```9b6918af```](https://github.com/ktmeaton/plague-phylogeography/commit/9b6918af) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
+* [```2d830a86```](https://github.com/ktmeaton/plague-phylogeography/commit/2d830a86) mark 2020 samples as low cov
+* [```7dfacc85```](https://github.com/ktmeaton/plague-phylogeography/commit/7dfacc85) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
+* [```77327b41```](https://github.com/ktmeaton/plague-phylogeography/commit/77327b41) add latvia samples to db
+* [```7422462a```](https://github.com/ktmeaton/plague-phylogeography/commit/7422462a) add site concordance factor analysis
+* [```4a4956ed```](https://github.com/ktmeaton/plague-phylogeography/commit/4a4956ed) notes about sample merging
+* [```295f1ecb```](https://github.com/ktmeaton/plague-phylogeography/commit/295f1ecb) fix study label
+* [```5cf3021e```](https://github.com/ktmeaton/plague-phylogeography/commit/5cf3021e) sweep commit for writing
+* [```27390bd8```](https://github.com/ktmeaton/plague-phylogeography/commit/27390bd8) update study comparison
+* [```39f8e123```](https://github.com/ktmeaton/plague-phylogeography/commit/39f8e123) add bezier to environment
+* [```975aa29d```](https://github.com/ktmeaton/plague-phylogeography/commit/975aa29d) sanity commit for timetree
+* [```f5035dac```](https://github.com/ktmeaton/plague-phylogeography/commit/f5035dac) fix timetree extension
+* [```3f89454a```](https://github.com/ktmeaton/plague-phylogeography/commit/3f89454a) map plotting in timetree
+* [```4cae6a50```](https://github.com/ktmeaton/plague-phylogeography/commit/4cae6a50) update mugration with lat lon
+* [```e7a31024```](https://github.com/ktmeaton/plague-phylogeography/commit/e7a31024) mugration cleanup
+* [```ccc54c5b```](https://github.com/ktmeaton/plague-phylogeography/commit/ccc54c5b) branch support cleanup
+* [```ff3aae35```](https://github.com/ktmeaton/plague-phylogeography/commit/ff3aae35) parse tree cleanup
+* [```4b16b285```](https://github.com/ktmeaton/plague-phylogeography/commit/4b16b285) plot study comparison
+* [```25526060```](https://github.com/ktmeaton/plague-phylogeography/commit/25526060) new color pal for geo
+* [```c6f860cc```](https://github.com/ktmeaton/plague-phylogeography/commit/c6f860cc) geo plot now with tree
+* [```8f690a7b```](https://github.com/ktmeaton/plague-phylogeography/commit/8f690a7b) update parse_tree metadata
+* [```1d597542```](https://github.com/ktmeaton/plague-phylogeography/commit/1d597542) fix bad notebook merge
+* [```b85d5fd5```](https://github.com/ktmeaton/plague-phylogeography/commit/b85d5fd5) new map and timeline
+* [```d5d8b680```](https://github.com/ktmeaton/plague-phylogeography/commit/d5d8b680) 2020 metadata and plot ancient on world
+* [```726a7b90```](https://github.com/ktmeaton/plague-phylogeography/commit/726a7b90) new metadata for 2020
+* [```9ccb3cd1```](https://github.com/ktmeaton/plague-phylogeography/commit/9ccb3cd1) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```2c3d5374```](https://github.com/ktmeaton/plague-phylogeography/commit/2c3d5374) test new method for combining/collapsing records
+* [```e1e97cd3```](https://github.com/ktmeaton/plague-phylogeography/commit/e1e97cd3) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```d6957a82```](https://github.com/ktmeaton/plague-phylogeography/commit/d6957a82) set pip user in bashrc
+* [```571e32a9```](https://github.com/ktmeaton/plague-phylogeography/commit/571e32a9) set pip user in bashrc
+* [```87b66813```](https://github.com/ktmeaton/plague-phylogeography/commit/87b66813) fix Ancient SRA comment
+* [```6bf94dc0```](https://github.com/ktmeaton/plague-phylogeography/commit/6bf94dc0) finish update geo date strain for 2020 biosample
+* [```c6f06331```](https://github.com/ktmeaton/plague-phylogeography/commit/c6f06331) update to 2020 db
+* [```7811f17a```](https://github.com/ktmeaton/plague-phylogeography/commit/7811f17a) update to 2020 db
+* [```5b77ceeb```](https://github.com/ktmeaton/plague-phylogeography/commit/5b77ceeb) updated geo metadata for Sečuán
+* [```2833302b```](https://github.com/ktmeaton/plague-phylogeography/commit/2833302b) fix geocode for Sečuán province
+* [```3240a098```](https://github.com/ktmeaton/plague-phylogeography/commit/3240a098) add study comparison geo map
+* [```0a7a1216```](https://github.com/ktmeaton/plague-phylogeography/commit/0a7a1216) add comment and rename metadata file, fix latest config
+* [```e0f678e1```](https://github.com/ktmeaton/plague-phylogeography/commit/e0f678e1) package lock
+* [```32a1f534```](https://github.com/ktmeaton/plague-phylogeography/commit/32a1f534) suspicious merge
+* [```dd29e926```](https://github.com/ktmeaton/plague-phylogeography/commit/dd29e926) sanity commit before working on heatmap
+* [```f8072798```](https://github.com/ktmeaton/plague-phylogeography/commit/f8072798) mugration uses config and color_tree
+* [```875800ac```](https://github.com/ktmeaton/plague-phylogeography/commit/875800ac) branch_support uses config
+* [```44080fa6```](https://github.com/ktmeaton/plague-phylogeography/commit/44080fa6) parse_tree now uses config
+* [```7652acad```](https://github.com/ktmeaton/plague-phylogeography/commit/7652acad) timetree plots before using config
+* [```16dae928```](https://github.com/ktmeaton/plague-phylogeography/commit/16dae928) mugration standardize ladderize and svg
+* [```0518f6c4```](https://github.com/ktmeaton/plague-phylogeography/commit/0518f6c4) branch_support standardize ladderize and svg
+* [```270f16e5```](https://github.com/ktmeaton/plague-phylogeography/commit/270f16e5) parse tree try to standardize ladderize
+* [```27c775b8```](https://github.com/ktmeaton/plague-phylogeography/commit/27c775b8) svg test for markdown
+* [```3745055f```](https://github.com/ktmeaton/plague-phylogeography/commit/3745055f) sanity commit of workbooks and output
+* [```aba58c2b```](https://github.com/ktmeaton/plague-phylogeography/commit/aba58c2b) test mugration auspice
+* [```29e591bb```](https://github.com/ktmeaton/plague-phylogeography/commit/29e591bb) add latlons to parse tree
+* [```e49af9d0```](https://github.com/ktmeaton/plague-phylogeography/commit/e49af9d0) test parse tree auspice online
+* [```486127bd```](https://github.com/ktmeaton/plague-phylogeography/commit/486127bd) make a comprehensive auspice config
+* [```14ba674d```](https://github.com/ktmeaton/plague-phylogeography/commit/14ba674d) add mugration results to docs
+* [```bfc575af```](https://github.com/ktmeaton/plague-phylogeography/commit/bfc575af) add parse tree results
+* [```cf941a98```](https://github.com/ktmeaton/plague-phylogeography/commit/cf941a98) notebooks export json for auspice
+* [```d17e947a```](https://github.com/ktmeaton/plague-phylogeography/commit/d17e947a) update branch_support with script name
+* [```7764585c```](https://github.com/ktmeaton/plague-phylogeography/commit/7764585c) configure npm as root user before installing
+* [```f93ed6f6```](https://github.com/ktmeaton/plague-phylogeography/commit/f93ed6f6) export json files using dataframe
+* [```7a6b7fed```](https://github.com/ktmeaton/plague-phylogeography/commit/7a6b7fed) add augur to conda env and auspice to dockerfile
+* [```142b7d8d```](https://github.com/ktmeaton/plague-phylogeography/commit/142b7d8d) fix missing node names and export to json
+* [```c2f86ede```](https://github.com/ktmeaton/plague-phylogeography/commit/c2f86ede) add json python scripts
+* [```d456d4fc```](https://github.com/ktmeaton/plague-phylogeography/commit/d456d4fc) save subtree outputs before fixing second pandemic fig
+* [```c5ecbe6f```](https://github.com/ktmeaton/plague-phylogeography/commit/c5ecbe6f) more elegant plotting
+* [```4f3672ff```](https://github.com/ktmeaton/plague-phylogeography/commit/4f3672ff) add r2 to regression
+* [```de7742b8```](https://github.com/ktmeaton/plague-phylogeography/commit/de7742b8) divtree timetree comparison
+* [```290e5207```](https://github.com/ktmeaton/plague-phylogeography/commit/290e5207) nice timetree with nodes and events
+* [```2937112d```](https://github.com/ktmeaton/plague-phylogeography/commit/2937112d) rename timetree_rtt
+* [```349cf19b```](https://github.com/ktmeaton/plague-phylogeography/commit/349cf19b) finally working timetree
+* [```581b6768```](https://github.com/ktmeaton/plague-phylogeography/commit/581b6768) plotting improvements but stats worsen
+* [```78b21448```](https://github.com/ktmeaton/plague-phylogeography/commit/78b21448) start of functional timetree
+* [```26e139e1```](https://github.com/ktmeaton/plague-phylogeography/commit/26e139e1) successful clock_filter and rtt plot
+* [```db25adfc```](https://github.com/ktmeaton/plague-phylogeography/commit/db25adfc) trying to figure out root branch length
+* [```2844f039```](https://github.com/ktmeaton/plague-phylogeography/commit/2844f039) add geopandas descartes and contextily
+* [```9d85a2d8```](https://github.com/ktmeaton/plague-phylogeography/commit/9d85a2d8) remove old large report
+* [```6dd02cbf```](https://github.com/ktmeaton/plague-phylogeography/commit/6dd02cbf) remove old example folder
+* [```df33c25f```](https://github.com/ktmeaton/plague-phylogeography/commit/df33c25f) add snippy multi extract report caption
+* [```3439f44e```](https://github.com/ktmeaton/plague-phylogeography/commit/3439f44e) add a constant sites file for alignment
+* [```0fb9c76f```](https://github.com/ktmeaton/plague-phylogeography/commit/0fb9c76f) testing of geo mugration and timetree before vcf
+* [```106f77db```](https://github.com/ktmeaton/plague-phylogeography/commit/106f77db) work on contextily tiles
+* [```bc2714ed```](https://github.com/ktmeaton/plague-phylogeography/commit/bc2714ed) exciting geo progress!
+* [```46cc418e```](https://github.com/ktmeaton/plague-phylogeography/commit/46cc418e) test geopandas plotting
+* [```4a15bdeb```](https://github.com/ktmeaton/plague-phylogeography/commit/4a15bdeb) start geo work
+* [```675862a0```](https://github.com/ktmeaton/plague-phylogeography/commit/675862a0) plot tips
+* [```500eab36```](https://github.com/ktmeaton/plague-phylogeography/commit/500eab36) plot tree always by div
+* [```ed351658```](https://github.com/ktmeaton/plague-phylogeography/commit/ed351658) better scaling of tree plots
+* [```76eb5c09```](https://github.com/ktmeaton/plague-phylogeography/commit/76eb5c09) use proper pandas df updating with at
+* [```5634b363```](https://github.com/ktmeaton/plague-phylogeography/commit/5634b363) new noteboook results
+* [```c3297e30```](https://github.com/ktmeaton/plague-phylogeography/commit/c3297e30) new result with bam_depth set properly
+* [```1effc299```](https://github.com/ktmeaton/plague-phylogeography/commit/1effc299) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
+* [```4781b143```](https://github.com/ktmeaton/plague-phylogeography/commit/4781b143) add plot het scripts
+* [```1614d9d0```](https://github.com/ktmeaton/plague-phylogeography/commit/1614d9d0) back up results 2021-01-15
+* [```f440709d```](https://github.com/ktmeaton/plague-phylogeography/commit/f440709d) mark 2 samples as excess het
+* [```6003795d```](https://github.com/ktmeaton/plague-phylogeography/commit/6003795d) fix bam depth in snippy pairwise
+* [```65d9de44```](https://github.com/ktmeaton/plague-phylogeography/commit/65d9de44) remove old docs results folders
+* [```a85613d9```](https://github.com/ktmeaton/plague-phylogeography/commit/a85613d9) upload latest notebooks and results
+* [```7c9f92d2```](https://github.com/ktmeaton/plague-phylogeography/commit/7c9f92d2) list jupyter notebooks
+* [```a70168a5```](https://github.com/ktmeaton/plague-phylogeography/commit/a70168a5) update branch support notebook
+* [```4ae1e84a```](https://github.com/ktmeaton/plague-phylogeography/commit/4ae1e84a) create new notebook and output for branch support
+* [```95d46c81```](https://github.com/ktmeaton/plague-phylogeography/commit/95d46c81) remove other attr from phyloxml parse
+* [```e57f1810```](https://github.com/ktmeaton/plague-phylogeography/commit/e57f1810) save branch support before change to tree_df
+* [```93848339```](https://github.com/ktmeaton/plague-phylogeography/commit/93848339) remove redundant files that are in report
+* [```37d7c970```](https://github.com/ktmeaton/plague-phylogeography/commit/37d7c970) add latest snippy multi
+* [```a901fe71```](https://github.com/ktmeaton/plague-phylogeography/commit/a901fe71) add latest iqtree
+* [```4ea1cbe9```](https://github.com/ktmeaton/plague-phylogeography/commit/4ea1cbe9) add latest metadata
+* [```afc06a6d```](https://github.com/ktmeaton/plague-phylogeography/commit/afc06a6d) add latest multiqc
+* [```a2b3f3ab```](https://github.com/ktmeaton/plague-phylogeography/commit/a2b3f3ab) more output and plotting for mug
+* [```2bd0b350```](https://github.com/ktmeaton/plague-phylogeography/commit/2bd0b350) mugration notebook to use loops
+* [```4d4876c0```](https://github.com/ktmeaton/plague-phylogeography/commit/4d4876c0) export branch support tree df
+* [```47902e57```](https://github.com/ktmeaton/plague-phylogeography/commit/47902e57) add branch_support results
+* [```21d8bea6```](https://github.com/ktmeaton/plague-phylogeography/commit/21d8bea6) remove pyqt and ete3
+* [```636003f5```](https://github.com/ktmeaton/plague-phylogeography/commit/636003f5) remove pyqt and ete3
+* [```079efcac```](https://github.com/ktmeaton/plague-phylogeography/commit/079efcac) reset default missing data to 50 for CI
+* [```531abb92```](https://github.com/ktmeaton/plague-phylogeography/commit/531abb92) add plot_missing_data to all target
+* [```37580d67```](https://github.com/ktmeaton/plague-phylogeography/commit/37580d67) make a latest results folder
+* [```24f3a9e8```](https://github.com/ktmeaton/plague-phylogeography/commit/24f3a9e8) save a production config
+* [```0b36590c```](https://github.com/ktmeaton/plague-phylogeography/commit/0b36590c) try new targets and all
+* [```4507e7da```](https://github.com/ktmeaton/plague-phylogeography/commit/4507e7da) simplify default snakemake.yaml
+* [```7f767ea2```](https://github.com/ktmeaton/plague-phylogeography/commit/7f767ea2) experiment with ete3 and pyqt
+* [```a12d58e9```](https://github.com/ktmeaton/plague-phylogeography/commit/a12d58e9) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```9d796181```](https://github.com/ktmeaton/plague-phylogeography/commit/9d796181) remove duplicate strains
+* [```a002babf```](https://github.com/ktmeaton/plague-phylogeography/commit/a002babf) mugration on branch major
+* [```f118f9ae```](https://github.com/ktmeaton/plague-phylogeography/commit/f118f9ae) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```001ec7cf```](https://github.com/ktmeaton/plague-phylogeography/commit/001ec7cf) fix S3 branch
+* [```4024e108```](https://github.com/ktmeaton/plague-phylogeography/commit/4024e108) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```84ea42a6```](https://github.com/ktmeaton/plague-phylogeography/commit/84ea42a6) last tidy up of branch info
+* [```48db2a15```](https://github.com/ktmeaton/plague-phylogeography/commit/48db2a15) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```bfd11269```](https://github.com/ktmeaton/plague-phylogeography/commit/bfd11269) complete branch annotation
+* [```2237db98```](https://github.com/ktmeaton/plague-phylogeography/commit/2237db98) edit all MED
+* [```18ede7e6```](https://github.com/ktmeaton/plague-phylogeography/commit/18ede7e6) edit to 2.ANT3
+* [```a2eb6c7c```](https://github.com/ktmeaton/plague-phylogeography/commit/a2eb6c7c) edit branches Bronze Age 0.PE7 0.PE2 0.PE4
+* [```9ca23615```](https://github.com/ktmeaton/plague-phylogeography/commit/9ca23615) version control black
+* [```f62ff25f```](https://github.com/ktmeaton/plague-phylogeography/commit/f62ff25f) lint with black v 19
+* [```2c20792c```](https://github.com/ktmeaton/plague-phylogeography/commit/2c20792c) try to include branch in metadata
+* [```00e1cd54```](https://github.com/ktmeaton/plague-phylogeography/commit/00e1cd54) simplify BioSampleBranch
+* [```435eb658```](https://github.com/ktmeaton/plague-phylogeography/commit/435eb658) finish keller2019 comments
+* [```8231bd03```](https://github.com/ktmeaton/plague-phylogeography/commit/8231bd03) BiosampleBranch Part 11
+* [```47613b3c```](https://github.com/ktmeaton/plague-phylogeography/commit/47613b3c) BiosampleBranch Part 10
+* [```ccd49978```](https://github.com/ktmeaton/plague-phylogeography/commit/ccd49978) BiosampleBranch Part 9
+* [```32bb5b4b```](https://github.com/ktmeaton/plague-phylogeography/commit/32bb5b4b) BiosampleBranch Part 8
+* [```5df5a210```](https://github.com/ktmeaton/plague-phylogeography/commit/5df5a210) BiosampleBranch Part 7
+* [```dfe73c43```](https://github.com/ktmeaton/plague-phylogeography/commit/dfe73c43) BiosampleBranch Part 6
+* [```d54dfe9f```](https://github.com/ktmeaton/plague-phylogeography/commit/d54dfe9f) BiosampleBranch Part 5
+* [```7dfd88ae```](https://github.com/ktmeaton/plague-phylogeography/commit/7dfd88ae) BiosampleBranch Part 4
+* [```7e414e40```](https://github.com/ktmeaton/plague-phylogeography/commit/7e414e40) BiosampleBranch Part 3
+* [```a1c86f26```](https://github.com/ktmeaton/plague-phylogeography/commit/a1c86f26) disable cartopy for now
+* [```8aa36585```](https://github.com/ktmeaton/plague-phylogeography/commit/8aa36585) BiosampleBranch Part 2
+* [```5e871599```](https://github.com/ktmeaton/plague-phylogeography/commit/5e871599) BiosampleBranch Part 1
+* [```b1b453bb```](https://github.com/ktmeaton/plague-phylogeography/commit/b1b453bb) add biosample column BioSampleBranch
+* [```52137db2```](https://github.com/ktmeaton/plague-phylogeography/commit/52137db2) think about cartopy
+* [```e0ad89bd```](https://github.com/ktmeaton/plague-phylogeography/commit/e0ad89bd) use province for joint plot
+* [```a70dbb8f```](https://github.com/ktmeaton/plague-phylogeography/commit/a70dbb8f) make kde y more sensitive
+* [```d9cb3dbd```](https://github.com/ktmeaton/plague-phylogeography/commit/d9cb3dbd) make kde y more sensitive
+* [```b2f67742```](https://github.com/ktmeaton/plague-phylogeography/commit/b2f67742) make kde y more sensitive
+* [```d7e654b5```](https://github.com/ktmeaton/plague-phylogeography/commit/d7e654b5) resize joint points
+* [```cb5517ee```](https://github.com/ktmeaton/plague-phylogeography/commit/cb5517ee) add joint label and kde
+* [```ae8a5f60```](https://github.com/ktmeaton/plague-phylogeography/commit/ae8a5f60) update seaborn for variance bug
+* [```37066272```](https://github.com/ktmeaton/plague-phylogeography/commit/37066272) new analysis with captions
+* [```0a101cee```](https://github.com/ktmeaton/plague-phylogeography/commit/0a101cee) add seaborn plotting
+* [```6812f207```](https://github.com/ktmeaton/plague-phylogeography/commit/6812f207) comprehensive branch support plot
+* [```15c970fe```](https://github.com/ktmeaton/plague-phylogeography/commit/15c970fe) new legends for confidence
+* [```08ffd22d```](https://github.com/ktmeaton/plague-phylogeography/commit/08ffd22d) add country histogram
+* [```539cf924```](https://github.com/ktmeaton/plague-phylogeography/commit/539cf924) test country mugration
+* [```dfa23bfe```](https://github.com/ktmeaton/plague-phylogeography/commit/dfa23bfe) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```58550fe9```](https://github.com/ktmeaton/plague-phylogeography/commit/58550fe9) update Mongolia foci
+* [```2d2696f4```](https://github.com/ktmeaton/plague-phylogeography/commit/2d2696f4) run country mugration
+* [```387fa8f6```](https://github.com/ktmeaton/plague-phylogeography/commit/387fa8f6) improve attr writing to sml
+* [```97955d5d```](https://github.com/ktmeaton/plague-phylogeography/commit/97955d5d) create jpg instead of png
+* [```ccd4d74f```](https://github.com/ktmeaton/plague-phylogeography/commit/ccd4d74f) add mugration biovar notebook and output
+* [```d39b36b8```](https://github.com/ktmeaton/plague-phylogeography/commit/d39b36b8) treetime notebook draft
+* [```7e6db5f7```](https://github.com/ktmeaton/plague-phylogeography/commit/7e6db5f7) extra pre-commit install step
+* [```99100096```](https://github.com/ktmeaton/plague-phylogeography/commit/99100096) move docs images folder
+* [```f8bd2ac8```](https://github.com/ktmeaton/plague-phylogeography/commit/f8bd2ac8) Fix get-diff ver typo
+* [```886df5ed```](https://github.com/ktmeaton/plague-phylogeography/commit/886df5ed) update docker action git diff ver
+* [```809eaa7a```](https://github.com/ktmeaton/plague-phylogeography/commit/809eaa7a) improve treetime tree parsing and renaming
+* [```87c63db8```](https://github.com/ktmeaton/plague-phylogeography/commit/87c63db8) fix treetime typo
+* [```f701caef```](https://github.com/ktmeaton/plague-phylogeography/commit/f701caef) update Azerbaijan province
+* [```6613527b```](https://github.com/ktmeaton/plague-phylogeography/commit/6613527b) update India date
+* [```8f0126bd```](https://github.com/ktmeaton/plague-phylogeography/commit/8f0126bd) update db with monoglia province fix
+* [```0ec7f33b```](https://github.com/ktmeaton/plague-phylogeography/commit/0ec7f33b) add treetime to env
+* [```973a0e5e```](https://github.com/ktmeaton/plague-phylogeography/commit/973a0e5e) better messages for init
+* [```e43e21b4```](https://github.com/ktmeaton/plague-phylogeography/commit/e43e21b4) better messages for init
+* [```e1bcb967```](https://github.com/ktmeaton/plague-phylogeography/commit/e1bcb967) try line wrap
+* [```05b12afa```](https://github.com/ktmeaton/plague-phylogeography/commit/05b12afa) try to update gitpod init
+* [```81e8615f```](https://github.com/ktmeaton/plague-phylogeography/commit/81e8615f) update singularity for action pipeline CI
+* [```8b1432bf```](https://github.com/ktmeaton/plague-phylogeography/commit/8b1432bf) update singularity action
+* [```efacc2d5```](https://github.com/ktmeaton/plague-phylogeography/commit/efacc2d5) update miniconda for action pipeline CI
+* [```acc4dfdc```](https://github.com/ktmeaton/plague-phylogeography/commit/acc4dfdc) update miniconda action
+* [```c27c6e33```](https://github.com/ktmeaton/plague-phylogeography/commit/c27c6e33) try to init pre-commit in gitpod
+* [```90a29b25```](https://github.com/ktmeaton/plague-phylogeography/commit/90a29b25) Update .gitpod.yml
+* [```5606e1b0```](https://github.com/ktmeaton/plague-phylogeography/commit/5606e1b0) use repo docker image
+* [```0fb62cb6```](https://github.com/ktmeaton/plague-phylogeography/commit/0fb62cb6) Update .gitpod.yml
+* [```d6c4ed7b```](https://github.com/ktmeaton/plague-phylogeography/commit/d6c4ed7b) Merge pull request #1 from ktmeaton/ktmeaton/gitpod-setup
+* [```f5a23112```](https://github.com/ktmeaton/plague-phylogeography/commit/f5a23112) Fully automate dev setup with Gitpod
+* [```c0073b4e```](https://github.com/ktmeaton/plague-phylogeography/commit/c0073b4e) more columns in metadata
+* [```87bf34b5```](https://github.com/ktmeaton/plague-phylogeography/commit/87bf34b5) consolidate date format
+* [```66d3ce73```](https://github.com/ktmeaton/plague-phylogeography/commit/66d3ce73) fix ancient date format
+* [```1cd4fab4```](https://github.com/ktmeaton/plague-phylogeography/commit/1cd4fab4) fix ancient date format
+* [```0941b21f```](https://github.com/ktmeaton/plague-phylogeography/commit/0941b21f) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```3af76c71```](https://github.com/ktmeaton/plague-phylogeography/commit/3af76c71) finish geocoding ancient samples
+* [```ca445d18```](https://github.com/ktmeaton/plague-phylogeography/commit/ca445d18) remove site workflow
+* [```2756d455```](https://github.com/ktmeaton/plague-phylogeography/commit/2756d455) remove old docs workflow
+* [```9a9ef21b```](https://github.com/ktmeaton/plague-phylogeography/commit/9a9ef21b) detect docker node
+* [```f36534a4```](https://github.com/ktmeaton/plague-phylogeography/commit/f36534a4) add env IN_DOCKER_CONTAINER to dockerfile
+* [```469b66db```](https://github.com/ktmeaton/plague-phylogeography/commit/469b66db) more ancient annotations
+* [```a740d08f```](https://github.com/ktmeaton/plague-phylogeography/commit/a740d08f) start geocoding ancient samples
+* [```729d50e5```](https://github.com/ktmeaton/plague-phylogeography/commit/729d50e5) mark download_sra as a local rule
+* [```42efacc6```](https://github.com/ktmeaton/plague-phylogeography/commit/42efacc6) update profiles with flowdash bio script
+* [```ed2f521b```](https://github.com/ktmeaton/plague-phylogeography/commit/ed2f521b) add logic for dry run logging
+* [```eeda3a96```](https://github.com/ktmeaton/plague-phylogeography/commit/eeda3a96) add sql query limit to avoid REMOVE SRA samples
+* [```1ade32f5```](https://github.com/ktmeaton/plague-phylogeography/commit/1ade32f5) begin comments for SRA Modern
+* [```1cb0f696```](https://github.com/ktmeaton/plague-phylogeography/commit/1cb0f696) add geopy to environment and docs
+* [```b417262b```](https://github.com/ktmeaton/plague-phylogeography/commit/b417262b) update sra modern comments to TBD
+* [```9a39468e```](https://github.com/ktmeaton/plague-phylogeography/commit/9a39468e) try add flowdash bio cred at docker runtime
+* [```cd15c18a```](https://github.com/ktmeaton/plague-phylogeography/commit/cd15c18a) try putting docker flowdash cred in .env file
+* [```9050e9db```](https://github.com/ktmeaton/plague-phylogeography/commit/9050e9db) add flowdash cred to pipeline env
+* [```c20bf1da```](https://github.com/ktmeaton/plague-phylogeography/commit/c20bf1da) better help message for missing token or username
+* [```015270ba```](https://github.com/ktmeaton/plague-phylogeography/commit/015270ba) add flowdash bio secrets to gh
+* [```8018466d```](https://github.com/ktmeaton/plague-phylogeography/commit/8018466d) update workflow param for flowdash-bio
+* [```fece7da3```](https://github.com/ktmeaton/plague-phylogeography/commit/fece7da3) fix target for plot
+* [```a1489fd0```](https://github.com/ktmeaton/plague-phylogeography/commit/a1489fd0) start work on flowdash-bio logging
+* [```5afa2a5f```](https://github.com/ktmeaton/plague-phylogeography/commit/5afa2a5f) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```633e9a89```](https://github.com/ktmeaton/plague-phylogeography/commit/633e9a89) start making log script for flowdash-bio
+* [```04187fda```](https://github.com/ktmeaton/plague-phylogeography/commit/04187fda) Create pdf of treefile
+* [```c2a3be4f```](https://github.com/ktmeaton/plague-phylogeography/commit/c2a3be4f) rearrange and add metadata
+* [```efc513ff```](https://github.com/ktmeaton/plague-phylogeography/commit/efc513ff) results for 2020-11-09
+* [```d370523c```](https://github.com/ktmeaton/plague-phylogeography/commit/d370523c) add new snippy log files
+* [```5588d37a```](https://github.com/ktmeaton/plague-phylogeography/commit/5588d37a) rename docs
+* [```55265b22```](https://github.com/ktmeaton/plague-phylogeography/commit/55265b22) store important results in docs
+* [```6f983240```](https://github.com/ktmeaton/plague-phylogeography/commit/6f983240) change some variants to line rather than scatter
+* [```468aa3bd```](https://github.com/ktmeaton/plague-phylogeography/commit/468aa3bd) tidy up parsing filtered
+* [```4604fae1```](https://github.com/ktmeaton/plague-phylogeography/commit/4604fae1) update plotting script
+* [```aa801366```](https://github.com/ktmeaton/plague-phylogeography/commit/aa801366) log passing and failing sites
+* [```fa00709d```](https://github.com/ktmeaton/plague-phylogeography/commit/fa00709d) allow keeping singletons in script
+* [```47dcd7d4```](https://github.com/ktmeaton/plague-phylogeography/commit/47dcd7d4) filter singleton sites
+* [```e2f34a87```](https://github.com/ktmeaton/plague-phylogeography/commit/e2f34a87) add logs to report file
+* [```a00d581a```](https://github.com/ktmeaton/plague-phylogeography/commit/a00d581a) clean up results files now in report
+* [```3b090b88```](https://github.com/ktmeaton/plague-phylogeography/commit/3b090b88) now with multiqc report
+* [```4f9b22c9```](https://github.com/ktmeaton/plague-phylogeography/commit/4f9b22c9) upgrade nodejs and add nbconvert
+* [```1d39c723```](https://github.com/ktmeaton/plague-phylogeography/commit/1d39c723) second draft phylogeny filtering
+* [```00fc1203```](https://github.com/ktmeaton/plague-phylogeography/commit/00fc1203) update missing data to have sites in title
+* [```56dcdc4c```](https://github.com/ktmeaton/plague-phylogeography/commit/56dcdc4c) enable ability to pre-specify iqtree model
+* [```3029ef4b```](https://github.com/ktmeaton/plague-phylogeography/commit/3029ef4b) enable ability to pre-specify iqtree model
+* [```1f9d14bb```](https://github.com/ktmeaton/plague-phylogeography/commit/1f9d14bb) run pipelin workflow if config changes
+* [```54be337d```](https://github.com/ktmeaton/plague-phylogeography/commit/54be337d) restrict sql searches to non-empty cells
+* [```59ab96ab```](https://github.com/ktmeaton/plague-phylogeography/commit/59ab96ab) finalize assembly comments
+* [```3900055d```](https://github.com/ktmeaton/plague-phylogeography/commit/3900055d) don't upload logs by default
+* [```afcaf2e1```](https://github.com/ktmeaton/plague-phylogeography/commit/afcaf2e1) work on phylogeny comments
+* [```66187381```](https://github.com/ktmeaton/plague-phylogeography/commit/66187381) avoid using run rules for report errors
+* [```3902cf1f```](https://github.com/ktmeaton/plague-phylogeography/commit/3902cf1f) always upload logs, reinstate report for troubleshooting
+* [```34ec827f```](https://github.com/ktmeaton/plague-phylogeography/commit/34ec827f) test conda pipeline with clean
+* [```cd02a240```](https://github.com/ktmeaton/plague-phylogeography/commit/cd02a240) new metadata remove duplicates
+* [```145b3c56```](https://github.com/ktmeaton/plague-phylogeography/commit/145b3c56) remove duplicates from paths
+* [```2c67caf1```](https://github.com/ktmeaton/plague-phylogeography/commit/2c67caf1) fix missing _genomic
+* [```f2669cfd```](https://github.com/ktmeaton/plague-phylogeography/commit/f2669cfd) test metadata automation create
+* [```01d9f461```](https://github.com/ktmeaton/plague-phylogeography/commit/01d9f461) fix script rename
+* [```e876802e```](https://github.com/ktmeaton/plague-phylogeography/commit/e876802e) fix up all targets
+* [```a00b49e1```](https://github.com/ktmeaton/plague-phylogeography/commit/a00b49e1) try to fix plot all target
+* [```3305e76d```](https://github.com/ktmeaton/plague-phylogeography/commit/3305e76d) add metadata to all targets
+* [```54f7c2b7```](https://github.com/ktmeaton/plague-phylogeography/commit/54f7c2b7) more metadata updates
+* [```84ae6612```](https://github.com/ktmeaton/plague-phylogeography/commit/84ae6612) rename metadata script
+* [```77920d56```](https://github.com/ktmeaton/plague-phylogeography/commit/77920d56) add metadata creation rule
+* [```74b844f5```](https://github.com/ktmeaton/plague-phylogeography/commit/74b844f5) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```e9c76eae```](https://github.com/ktmeaton/plague-phylogeography/commit/e9c76eae) better paths for plot missing data
+* [```ed73783a```](https://github.com/ktmeaton/plague-phylogeography/commit/ed73783a) add missing data plotting to config
+* [```c6356307```](https://github.com/ktmeaton/plague-phylogeography/commit/c6356307) first draft of phylogeny
+* [```2b354c2d```](https://github.com/ktmeaton/plague-phylogeography/commit/2b354c2d) test for plotting missing_data
+* [```9a9c3006```](https://github.com/ktmeaton/plague-phylogeography/commit/9a9c3006) add scripts and env for plotly
+* [```a674d4f4```](https://github.com/ktmeaton/plague-phylogeography/commit/a674d4f4) improve filtering
+* [```f162c70d```](https://github.com/ktmeaton/plague-phylogeography/commit/f162c70d) missing data test
+* [```512b962c```](https://github.com/ktmeaton/plague-phylogeography/commit/512b962c) all multiqc report
+* [```380ede52```](https://github.com/ktmeaton/plague-phylogeography/commit/380ede52) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```dba7e9dd```](https://github.com/ktmeaton/plague-phylogeography/commit/dba7e9dd) html lint
+* [```41aa8e26```](https://github.com/ktmeaton/plague-phylogeography/commit/41aa8e26) update docs
+* [```e3ac335b```](https://github.com/ktmeaton/plague-phylogeography/commit/e3ac335b) linting update
+* [```a9cee5d2```](https://github.com/ktmeaton/plague-phylogeography/commit/a9cee5d2) disable report in pipeline workflow
+* [```cab1400e```](https://github.com/ktmeaton/plague-phylogeography/commit/cab1400e) filtered multiqc reports
+* [```ae5a1b50```](https://github.com/ktmeaton/plague-phylogeography/commit/ae5a1b50) back up multiqc
+* [```5051adb7```](https://github.com/ktmeaton/plague-phylogeography/commit/5051adb7) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
+* [```e163bb23```](https://github.com/ktmeaton/plague-phylogeography/commit/e163bb23) update sra report with better param
+* [```0243332a```](https://github.com/ktmeaton/plague-phylogeography/commit/0243332a) update manual tips
+* [```3f882d0c```](https://github.com/ktmeaton/plague-phylogeography/commit/3f882d0c) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
+* [```f555330b```](https://github.com/ktmeaton/plague-phylogeography/commit/f555330b) update manual edits docs
+* [```48089335```](https://github.com/ktmeaton/plague-phylogeography/commit/48089335) add local biosample records
+* [```64011651```](https://github.com/ktmeaton/plague-phylogeography/commit/64011651) finish all comments for sra ancient
+* [```bd1bdfc1```](https://github.com/ktmeaton/plague-phylogeography/commit/bd1bdfc1) new local report with coverage set to 10
+* [```4d83322d```](https://github.com/ktmeaton/plague-phylogeography/commit/4d83322d) new local multiqc report with fixed param
+* [```203f2268```](https://github.com/ktmeaton/plague-phylogeography/commit/203f2268) fix docs typos
+* [```40bd07d2```](https://github.com/ktmeaton/plague-phylogeography/commit/40bd07d2) docs update
+* [```e525b80b```](https://github.com/ktmeaton/plague-phylogeography/commit/e525b80b) test new snakemake with report reinstated
+* [```db159f7f```](https://github.com/ktmeaton/plague-phylogeography/commit/db159f7f) remove cutadapt from env
+* [```553e4738```](https://github.com/ktmeaton/plague-phylogeography/commit/553e4738) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
+* [```128afeb5```](https://github.com/ktmeaton/plague-phylogeography/commit/128afeb5) add local multiqc report
+* [```8b547445```](https://github.com/ktmeaton/plague-phylogeography/commit/8b547445) update jupyter notebooks
+* [```44bd273e```](https://github.com/ktmeaton/plague-phylogeography/commit/44bd273e) add all SRA Ancient comments
+* [```f65dbd5a```](https://github.com/ktmeaton/plague-phylogeography/commit/f65dbd5a) fix manual edit for GEN72
+* [```948c6650```](https://github.com/ktmeaton/plague-phylogeography/commit/948c6650) add cutadapt to env for manual edits
+* [```cdf1dd06```](https://github.com/ktmeaton/plague-phylogeography/commit/cdf1dd06) update docs for manual edits
+* [```4ed962d9```](https://github.com/ktmeaton/plague-phylogeography/commit/4ed962d9) add suffix all to multiqc reports
+* [```7c974781```](https://github.com/ktmeaton/plague-phylogeography/commit/7c974781) add suffix all to multiqc reports
+* [```5ecc8be3```](https://github.com/ktmeaton/plague-phylogeography/commit/5ecc8be3) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
+* [```09763f4f```](https://github.com/ktmeaton/plague-phylogeography/commit/09763f4f) add sra multiqc report
+* [```f5612743```](https://github.com/ktmeaton/plague-phylogeography/commit/f5612743) add ncbimeta to environment
+* [```d305f6d3```](https://github.com/ktmeaton/plague-phylogeography/commit/d305f6d3) update docs for local and sra
+* [```909ae265```](https://github.com/ktmeaton/plague-phylogeography/commit/909ae265) fix input fastq paths for eager
+* [```ba437a2a```](https://github.com/ktmeaton/plague-phylogeography/commit/ba437a2a) fix assembly ftp function counting error
+* [```3ee1c5d0```](https://github.com/ktmeaton/plague-phylogeography/commit/3ee1c5d0) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography into master
+* [```1e9a71ac```](https://github.com/ktmeaton/plague-phylogeography/commit/1e9a71ac) add assembly multiqc report
+* [```6b8df961```](https://github.com/ktmeaton/plague-phylogeography/commit/6b8df961) update sql commands and parse functions
+* [```6d97a4ec```](https://github.com/ktmeaton/plague-phylogeography/commit/6d97a4ec) fix typo in download_sra wildcards
+* [```35b04041```](https://github.com/ktmeaton/plague-phylogeography/commit/35b04041) working test of new path system
+* [```0436f1f1```](https://github.com/ktmeaton/plague-phylogeography/commit/0436f1f1) continue path reconfigure for all option
+* [```e3cb3c70```](https://github.com/ktmeaton/plague-phylogeography/commit/e3cb3c70) start working on new path function system
+* [```f448d23f```](https://github.com/ktmeaton/plague-phylogeography/commit/f448d23f) working on collect function
+* [```573931c1```](https://github.com/ktmeaton/plague-phylogeography/commit/573931c1) transition commit from laptop
+* [```4c69d76b```](https://github.com/ktmeaton/plague-phylogeography/commit/4c69d76b) formally update eager env to 2.2.1
+* [```023efc95```](https://github.com/ktmeaton/plague-phylogeography/commit/023efc95) better sql query
+* [```99aa1601```](https://github.com/ktmeaton/plague-phylogeography/commit/99aa1601) set default time_min to 6 hours for download_sra
+* [```37657055```](https://github.com/ktmeaton/plague-phylogeography/commit/37657055) remove report functionality until snakemake updated
+* [```3b525172```](https://github.com/ktmeaton/plague-phylogeography/commit/3b525172) actually add docker py test
+* [```14c63134```](https://github.com/ktmeaton/plague-phylogeography/commit/14c63134) also test docker python ver
+* [```e219d7dc```](https://github.com/ktmeaton/plague-phylogeography/commit/e219d7dc) test python modeule versions
+* [```8c0abb78```](https://github.com/ktmeaton/plague-phylogeography/commit/8c0abb78) change target names from test
+* [```6b8cfda7```](https://github.com/ktmeaton/plague-phylogeography/commit/6b8cfda7) change sql query and stamp eager to 2.2.1
+* [```a789ab76```](https://github.com/ktmeaton/plague-phylogeography/commit/a789ab76) convert docs from rst to markdown for main
+* [```07b6cf45```](https://github.com/ktmeaton/plague-phylogeography/commit/07b6cf45) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```1a132474```](https://github.com/ktmeaton/plague-phylogeography/commit/1a132474) add new comment structure and remove master tables in db
+* [```e1aa63b6```](https://github.com/ktmeaton/plague-phylogeography/commit/e1aa63b6) Merge and upload reports
+* [```dfb3f0ee```](https://github.com/ktmeaton/plague-phylogeography/commit/dfb3f0ee) big run reports and config
+* [```7a99b755```](https://github.com/ktmeaton/plague-phylogeography/commit/7a99b755) use vdb config to prepare for download
+* [```fcd158ab```](https://github.com/ktmeaton/plague-phylogeography/commit/fcd158ab) add file_acc info to download_sra msg
+* [```d5e7e948```](https://github.com/ktmeaton/plague-phylogeography/commit/d5e7e948) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```1134fda6```](https://github.com/ktmeaton/plague-phylogeography/commit/1134fda6) eager now ignores qualimap
+* [```4e1e0940```](https://github.com/ktmeaton/plague-phylogeography/commit/4e1e0940) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```3f0deda4```](https://github.com/ktmeaton/plague-phylogeography/commit/3f0deda4) update snakemake to 5.26.1 to deal with scheduler issues
+* [```b5c31633```](https://github.com/ktmeaton/plague-phylogeography/commit/b5c31633) remove qualimap from eager
+* [```b428f2fc```](https://github.com/ktmeaton/plague-phylogeography/commit/b428f2fc) try different eager move strategy
+* [```7c307eaa```](https://github.com/ktmeaton/plague-phylogeography/commit/7c307eaa) fix snippy multi missing in qualimap
+* [```c8ea5f0e```](https://github.com/ktmeaton/plague-phylogeography/commit/c8ea5f0e) fix multicore and multimem resources
+* [```b3fad8ec```](https://github.com/ktmeaton/plague-phylogeography/commit/b3fad8ec) improve multi core processing
+* [```418bdb4e```](https://github.com/ktmeaton/plague-phylogeography/commit/418bdb4e) user prefetch before fastq-dump
+* [```f8a62c87```](https://github.com/ktmeaton/plague-phylogeography/commit/f8a62c87) update time and script tsv for eager
+* [```303cc529```](https://github.com/ktmeaton/plague-phylogeography/commit/303cc529) bug fix for multiple file sra sample
+* [```09501c30```](https://github.com/ktmeaton/plague-phylogeography/commit/09501c30) mega reprt
+* [```5c192e1b```](https://github.com/ktmeaton/plague-phylogeography/commit/5c192e1b) update multiqc and set perl locale
+* [```5c5bb1db```](https://github.com/ktmeaton/plague-phylogeography/commit/5c5bb1db) update profiles
+* [```37ff722c```](https://github.com/ktmeaton/plague-phylogeography/commit/37ff722c) update infoserv profile
+* [```e4f2ea84```](https://github.com/ktmeaton/plague-phylogeography/commit/e4f2ea84) add nextflow log back in
+* [```d3f1f943```](https://github.com/ktmeaton/plague-phylogeography/commit/d3f1f943) add report creation and artifact upload
+* [```25fd12cb```](https://github.com/ktmeaton/plague-phylogeography/commit/25fd12cb) simplify pipelines to help and all
+* [```c2af37c1```](https://github.com/ktmeaton/plague-phylogeography/commit/c2af37c1) verbose eager and compute-canada profile update
+* [```a607ec18```](https://github.com/ktmeaton/plague-phylogeography/commit/a607ec18) add docker to pipelin
+* [```50b7318b```](https://github.com/ktmeaton/plague-phylogeography/commit/50b7318b) remove eager
+* [```a8f4863c```](https://github.com/ktmeaton/plague-phylogeography/commit/a8f4863c) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```0c608301```](https://github.com/ktmeaton/plague-phylogeography/commit/0c608301) fix typo in Dockerfile
+* [```de726f5b```](https://github.com/ktmeaton/plague-phylogeography/commit/de726f5b) update docs
+* [```445321b4```](https://github.com/ktmeaton/plague-phylogeography/commit/445321b4) install ps to dockerfile and run eager as dev
+* [```82babf87```](https://github.com/ktmeaton/plague-phylogeography/commit/82babf87) try to mount volume for docker
+* [```e10a1472```](https://github.com/ktmeaton/plague-phylogeography/commit/e10a1472) add docker to install test
+* [```a9d717da```](https://github.com/ktmeaton/plague-phylogeography/commit/a9d717da) add eager test
+* [```8f98d7cd```](https://github.com/ktmeaton/plague-phylogeography/commit/8f98d7cd) remove debugging, configure pipelin
+* [```490e1e33```](https://github.com/ktmeaton/plague-phylogeography/commit/490e1e33) initialize sra-toolkit config file
+* [```787cb51c```](https://github.com/ktmeaton/plague-phylogeography/commit/787cb51c) rearrange env and add docker authentication
+* [```a8e3ae40```](https://github.com/ktmeaton/plague-phylogeography/commit/a8e3ae40) use different tmate debugger
+* [```38f2e040```](https://github.com/ktmeaton/plague-phylogeography/commit/38f2e040) put debug session at end
+* [```3b99af76```](https://github.com/ktmeaton/plague-phylogeography/commit/3b99af76) disable log handler slack
+* [```32f8e257```](https://github.com/ktmeaton/plague-phylogeography/commit/32f8e257) move debug to help step
+* [```b546ac7b```](https://github.com/ktmeaton/plague-phylogeography/commit/b546ac7b) add debug session
+* [```eebb4722```](https://github.com/ktmeaton/plague-phylogeography/commit/eebb4722) see what happens with vdb-config interactive
+* [```742bd13d```](https://github.com/ktmeaton/plague-phylogeography/commit/742bd13d) update docs
+* [```fc7d0a96```](https://github.com/ktmeaton/plague-phylogeography/commit/fc7d0a96) update after laptop changes
+* [```e5f084dd```](https://github.com/ktmeaton/plague-phylogeography/commit/e5f084dd) add nf-core eager install
+* [```df2caf81```](https://github.com/ktmeaton/plague-phylogeography/commit/df2caf81) rearrange place of vdb config
+* [```201311da```](https://github.com/ktmeaton/plague-phylogeography/commit/201311da) correct dockerfile path
+* [```10193fe5```](https://github.com/ktmeaton/plague-phylogeography/commit/10193fe5) try merged conda workflow
+* [```4d7367f8```](https://github.com/ktmeaton/plague-phylogeography/commit/4d7367f8) try merged conda env
+* [```0ab56c2c```](https://github.com/ktmeaton/plague-phylogeography/commit/0ab56c2c) test docker file with eager built in
+* [```9f6b2515```](https://github.com/ktmeaton/plague-phylogeography/commit/9f6b2515) separate into push and release jobs
+* [```03ad8c13```](https://github.com/ktmeaton/plague-phylogeography/commit/03ad8c13) more complicated if check
+* [```bcd723f4```](https://github.com/ktmeaton/plague-phylogeography/commit/bcd723f4) more complicated if for push
+* [```ca5c63c7```](https://github.com/ktmeaton/plague-phylogeography/commit/ca5c63c7) test with simple if conditional
+* [```4d0c1d4f```](https://github.com/ktmeaton/plague-phylogeography/commit/4d0c1d4f) try to use prefix filter
+* [```a4961519```](https://github.com/ktmeaton/plague-phylogeography/commit/a4961519) exclude docker pipeline
+* [```b5215102```](https://github.com/ktmeaton/plague-phylogeography/commit/b5215102) change git diff files
+* [```62f01f0a```](https://github.com/ktmeaton/plague-phylogeography/commit/62f01f0a) add docker back to workflows
+* [```d6d9a0d4```](https://github.com/ktmeaton/plague-phylogeography/commit/d6d9a0d4) try dockerfile with uuid vdb setup
+* [```626cc164```](https://github.com/ktmeaton/plague-phylogeography/commit/626cc164) add eager to test pipeline
+* [```0314a1c5```](https://github.com/ktmeaton/plague-phylogeography/commit/0314a1c5) split up and simplify pipelin
+* [```b57b37b9```](https://github.com/ktmeaton/plague-phylogeography/commit/b57b37b9) dont use special env variable for CONDA
+* [```0a449325```](https://github.com/ktmeaton/plague-phylogeography/commit/0a449325) copy install to pipeline
+* [```da79e2cc```](https://github.com/ktmeaton/plague-phylogeography/commit/da79e2cc) reset to simple install
+* [```275cb5d1```](https://github.com/ktmeaton/plague-phylogeography/commit/275cb5d1) test splitting step by matrix
+* [```9f295ec5```](https://github.com/ktmeaton/plague-phylogeography/commit/9f295ec5) typos in install
+* [```20886e42```](https://github.com/ktmeaton/plague-phylogeography/commit/20886e42) test external env install
+* [```ba5fb7ba```](https://github.com/ktmeaton/plague-phylogeography/commit/ba5fb7ba) switch back to external container
+* [```ccb41484```](https://github.com/ktmeaton/plague-phylogeography/commit/ccb41484) reset containers for download_sra
+* [```410728df```](https://github.com/ktmeaton/plague-phylogeography/commit/410728df) fix matrix typo
+* [```96f04087```](https://github.com/ktmeaton/plague-phylogeography/commit/96f04087) remove caching
+* [```3e041321```](https://github.com/ktmeaton/plague-phylogeography/commit/3e041321) try to cache conda env
+* [```7c03bd79```](https://github.com/ktmeaton/plague-phylogeography/commit/7c03bd79) fix bash elif typo
+* [```e8ee49a8```](https://github.com/ktmeaton/plague-phylogeography/commit/e8ee49a8) try pipeline with new org
+* [```4f20468a```](https://github.com/ktmeaton/plague-phylogeography/commit/4f20468a) make install a matrix again
+* [```4f5da757```](https://github.com/ktmeaton/plague-phylogeography/commit/4f5da757) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```ea8d5ff4```](https://github.com/ktmeaton/plague-phylogeography/commit/ea8d5ff4) add singularity pull
+* [```f0acb9e2```](https://github.com/ktmeaton/plague-phylogeography/commit/f0acb9e2) update docs
+* [```378fdf0c```](https://github.com/ktmeaton/plague-phylogeography/commit/378fdf0c) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```e502b0e3```](https://github.com/ktmeaton/plague-phylogeography/commit/e502b0e3) add ftputil
+* [```dc6a5c4c```](https://github.com/ktmeaton/plague-phylogeography/commit/dc6a5c4c) update docs
+* [```17eca57e```](https://github.com/ktmeaton/plague-phylogeography/commit/17eca57e) move fail fast into strategy
+* [```9d392f33```](https://github.com/ktmeaton/plague-phylogeography/commit/9d392f33) move fail fast into strategy
+* [```c47f0728```](https://github.com/ktmeaton/plague-phylogeography/commit/c47f0728) install containers
+* [```77bead5c```](https://github.com/ktmeaton/plague-phylogeography/commit/77bead5c) separate jobs
+* [```7af97c18```](https://github.com/ktmeaton/plague-phylogeography/commit/7af97c18) try conditional with exclude
+* [```7b3ed018```](https://github.com/ktmeaton/plague-phylogeography/commit/7b3ed018) add gfortran
+* [```0ed03949```](https://github.com/ktmeaton/plague-phylogeography/commit/0ed03949) Update install.yaml
+* [```e036d452```](https://github.com/ktmeaton/plague-phylogeography/commit/e036d452) Change matrix if
+* [```ffa77816```](https://github.com/ktmeaton/plague-phylogeography/commit/ffa77816) test minimal install workflow
+* [```82b24382```](https://github.com/ktmeaton/plague-phylogeography/commit/82b24382) test env after qualimap change
+* [```7343171a```](https://github.com/ktmeaton/plague-phylogeography/commit/7343171a) rename default env
+* [```748af915```](https://github.com/ktmeaton/plague-phylogeography/commit/748af915) rename default env
+* [```1783521d```](https://github.com/ktmeaton/plague-phylogeography/commit/1783521d) disable plot libs
+* [```359124a5```](https://github.com/ktmeaton/plague-phylogeography/commit/359124a5) update conda and containers in rules
+* [```3fa270e7```](https://github.com/ktmeaton/plague-phylogeography/commit/3fa270e7) simplify env
+* [```e9662840```](https://github.com/ktmeaton/plague-phylogeography/commit/e9662840) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```3d7d828a```](https://github.com/ktmeaton/plague-phylogeography/commit/3d7d828a) use eager profiles singularity and conda
+* [```2e66be2b```](https://github.com/ktmeaton/plague-phylogeography/commit/2e66be2b) make nextflow executable
+* [```c2cf1471```](https://github.com/ktmeaton/plague-phylogeography/commit/c2cf1471) install nextflow
+* [```3c4992ee```](https://github.com/ktmeaton/plague-phylogeography/commit/3c4992ee) remove singularity defaults
+* [```2bea6719```](https://github.com/ktmeaton/plague-phylogeography/commit/2bea6719) try to use singularity with eager
+* [```44191f3e```](https://github.com/ktmeaton/plague-phylogeography/commit/44191f3e) try to use singularity with eager
+* [```4537e931```](https://github.com/ktmeaton/plague-phylogeography/commit/4537e931) fix default env cache
+* [```efd256ee```](https://github.com/ktmeaton/plague-phylogeography/commit/efd256ee) add containers to all rules
+* [```636db832```](https://github.com/ktmeaton/plague-phylogeography/commit/636db832) try disabling fail fast for matrix jobs
+* [```8149951a```](https://github.com/ktmeaton/plague-phylogeography/commit/8149951a) change default env name
+* [```2c68b2a5```](https://github.com/ktmeaton/plague-phylogeography/commit/2c68b2a5) try to label docker images with commit
+* [```fe02ede7```](https://github.com/ktmeaton/plague-phylogeography/commit/fe02ede7) fix container qc typo
+* [```539c667d```](https://github.com/ktmeaton/plague-phylogeography/commit/539c667d) give names to envs
+* [```0a900c20```](https://github.com/ktmeaton/plague-phylogeography/commit/0a900c20) change graham to cc with singularity
+* [```c5f6b55b```](https://github.com/ktmeaton/plague-phylogeography/commit/c5f6b55b) docker prep in workflow
+* [```5f4e0554```](https://github.com/ktmeaton/plague-phylogeography/commit/5f4e0554) docker and env overhaul
+* [```ab714433```](https://github.com/ktmeaton/plague-phylogeography/commit/ab714433) try build with matrix
+* [```e7ba66ad```](https://github.com/ktmeaton/plague-phylogeography/commit/e7ba66ad) try build with matrix
+* [```2675f96e```](https://github.com/ktmeaton/plague-phylogeography/commit/2675f96e) test matrix install
+* [```7c298d2d```](https://github.com/ktmeaton/plague-phylogeography/commit/7c298d2d) fix typo
+* [```fc250aaa```](https://github.com/ktmeaton/plague-phylogeography/commit/fc250aaa) test manual push
+* [```3a546126```](https://github.com/ktmeaton/plague-phylogeography/commit/3a546126) specify workdir
+* [```2888e3ff```](https://github.com/ktmeaton/plague-phylogeography/commit/2888e3ff) make sure conda activates in plot
+* [```85235e1f```](https://github.com/ktmeaton/plague-phylogeography/commit/85235e1f) make sure conda activates in plot
+* [```60d50443```](https://github.com/ktmeaton/plague-phylogeography/commit/60d50443) try push with gh action
+* [```c1a99b23```](https://github.com/ktmeaton/plague-phylogeography/commit/c1a99b23) try to push to docker hub
+* [```25fe5ce2```](https://github.com/ktmeaton/plague-phylogeography/commit/25fe5ce2) test run docker plot
+* [```8c8f503c```](https://github.com/ktmeaton/plague-phylogeography/commit/8c8f503c) test or operator
+* [```c31eb0e4```](https://github.com/ktmeaton/plague-phylogeography/commit/c31eb0e4) debug output 3
+* [```29f342e9```](https://github.com/ktmeaton/plague-phylogeography/commit/29f342e9) debug output 2
+* [```471e2f88```](https://github.com/ktmeaton/plague-phylogeography/commit/471e2f88) debug output
+* [```f928177c```](https://github.com/ktmeaton/plague-phylogeography/commit/f928177c) test contains operator
+* [```c7baccbf```](https://github.com/ktmeaton/plague-phylogeography/commit/c7baccbf) test contains operator
+* [```7a9d0d41```](https://github.com/ktmeaton/plague-phylogeography/commit/7a9d0d41) test if file change detected
+* [```77f56943```](https://github.com/ktmeaton/plague-phylogeography/commit/77f56943) filter take 2
+* [```245a68b9```](https://github.com/ktmeaton/plague-phylogeography/commit/245a68b9) try to restrict git diff files
+* [```231c01b9```](https://github.com/ktmeaton/plague-phylogeography/commit/231c01b9) check for changes before building
+* [```04fdd470```](https://github.com/ktmeaton/plague-phylogeography/commit/04fdd470) check changes test
+* [```5d35faea```](https://github.com/ktmeaton/plague-phylogeography/commit/5d35faea) fix paths in docker workflow
+* [```bfd5ab00```](https://github.com/ktmeaton/plague-phylogeography/commit/bfd5ab00) test docker init
+* [```e7658c49```](https://github.com/ktmeaton/plague-phylogeography/commit/e7658c49) try to fix mamba path
+* [```1af4b97d```](https://github.com/ktmeaton/plague-phylogeography/commit/1af4b97d) prepare for singularity
+* [```7d05f1b1```](https://github.com/ktmeaton/plague-phylogeography/commit/7d05f1b1) increase graham profile
+* [```e5283935```](https://github.com/ktmeaton/plague-phylogeography/commit/e5283935) add all target to testing
+* [```0b8f0043```](https://github.com/ktmeaton/plague-phylogeography/commit/0b8f0043) fix snippy multi filter target to snps
+* [```36f890e2```](https://github.com/ktmeaton/plague-phylogeography/commit/36f890e2) automate report upload
+* [```62591f8a```](https://github.com/ktmeaton/plague-phylogeography/commit/62591f8a) fix multiqc and qualimap dir targets
+* [```dcbffcf7```](https://github.com/ktmeaton/plague-phylogeography/commit/dcbffcf7) remove assembly print statement
+* [```3039c693```](https://github.com/ktmeaton/plague-phylogeography/commit/3039c693) remove test import
+* [```3ecb83bc```](https://github.com/ktmeaton/plague-phylogeography/commit/3ecb83bc) add table plot
+* [```f653b0bb```](https://github.com/ktmeaton/plague-phylogeography/commit/f653b0bb) iqtree and filter with new options
+* [```4c0dabbd```](https://github.com/ktmeaton/plague-phylogeography/commit/4c0dabbd) fix rstrip and rename local data
+* [```f0ab834d```](https://github.com/ktmeaton/plague-phylogeography/commit/f0ab834d) fix rstrip and rename local data
+* [```d3687aaf```](https://github.com/ktmeaton/plague-phylogeography/commit/d3687aaf) fix snippy pairwise wildcards
+* [```11dc463c```](https://github.com/ktmeaton/plague-phylogeography/commit/11dc463c) reorganize dir structure and troubleshoot eager
+* [```0585c54c```](https://github.com/ktmeaton/plague-phylogeography/commit/0585c54c) semi-colons
+* [```e30fb386```](https://github.com/ktmeaton/plague-phylogeography/commit/e30fb386) add merge snp density to workflow
+* [```1a7becba```](https://github.com/ktmeaton/plague-phylogeography/commit/1a7becba) fix bed merge input names
+* [```3d0361a1```](https://github.com/ktmeaton/plague-phylogeography/commit/3d0361a1) add snp density filtering
+* [```fe6d28f7```](https://github.com/ktmeaton/plague-phylogeography/commit/fe6d28f7) change threads to resources cpus
+* [```70aeecad```](https://github.com/ktmeaton/plague-phylogeography/commit/70aeecad) explictly set some rules to single core, log download_sra
+* [```ca7fbf0b```](https://github.com/ktmeaton/plague-phylogeography/commit/ca7fbf0b) remove loop from download_sra
+* [```69bc3738```](https://github.com/ktmeaton/plague-phylogeography/commit/69bc3738) try localrules and cacheing workflow env for pipelin
+* [```5159231b```](https://github.com/ktmeaton/plague-phylogeography/commit/5159231b) run install with workflow env cache
+* [```b0e9e729```](https://github.com/ktmeaton/plague-phylogeography/commit/b0e9e729) try restricted and parallel eager
+* [```0d7b5036```](https://github.com/ktmeaton/plague-phylogeography/commit/0d7b5036) add env file creation to install pipeline
+* [```ae41612d```](https://github.com/ktmeaton/plague-phylogeography/commit/ae41612d) use new conda profile complex
+* [```db61d63b```](https://github.com/ktmeaton/plague-phylogeography/commit/db61d63b) test new config
+* [```802a06b5```](https://github.com/ktmeaton/plague-phylogeography/commit/802a06b5) extend time
+* [```d06ade59```](https://github.com/ktmeaton/plague-phylogeography/commit/d06ade59) some fixes for nf-core/eager to avoid offline
+* [```7ad09edc```](https://github.com/ktmeaton/plague-phylogeography/commit/7ad09edc) reset eager channel order
+* [```b4b2fe26```](https://github.com/ktmeaton/plague-phylogeography/commit/b4b2fe26) use a slurm-specific status check script
+* [```e8a45d20```](https://github.com/ktmeaton/plague-phylogeography/commit/e8a45d20) update graham profile
+* [```78869e1d```](https://github.com/ktmeaton/plague-phylogeography/commit/78869e1d) remove nodes param and try NXF_OPTS
+* [```8a3d9ecf```](https://github.com/ktmeaton/plague-phylogeography/commit/8a3d9ecf) try to use wildcards.sample for graham log
+* [```a27c8298```](https://github.com/ktmeaton/plague-phylogeography/commit/a27c8298) update all profiles with generic config, change biosample to sample
+* [```b13fb3d5```](https://github.com/ktmeaton/plague-phylogeography/commit/b13fb3d5) reorganize config layout
+* [```bfa67866```](https://github.com/ktmeaton/plague-phylogeography/commit/bfa67866) working SLURM profile for graham
+* [```f1196d0a```](https://github.com/ktmeaton/plague-phylogeography/commit/f1196d0a) switch sbatch param to one line
+* [```dfd01693```](https://github.com/ktmeaton/plague-phylogeography/commit/dfd01693) slurm update after sbatch success
+* [```da8c6334```](https://github.com/ktmeaton/plague-phylogeography/commit/da8c6334) update slurm permissions
+* [```f5da2234```](https://github.com/ktmeaton/plague-phylogeography/commit/f5da2234) add slurm status check
+* [```aa7e5517```](https://github.com/ktmeaton/plague-phylogeography/commit/aa7e5517) remove partition param
+* [```631a3e84```](https://github.com/ktmeaton/plague-phylogeography/commit/631a3e84) hardcode prefix for logs
+* [```19b7934b```](https://github.com/ktmeaton/plague-phylogeography/commit/19b7934b) fix shadow prefix
+* [```cac3d9a7```](https://github.com/ktmeaton/plague-phylogeography/commit/cac3d9a7) remove threads config for snippy_pairwise
+* [```e3d971e7```](https://github.com/ktmeaton/plague-phylogeography/commit/e3d971e7) Merge docs
+* [```1636f8ed```](https://github.com/ktmeaton/plague-phylogeography/commit/1636f8ed) greater complexity to profiles
+* [```628faa90```](https://github.com/ktmeaton/plague-phylogeography/commit/628faa90) update docs
+* [```85d16613```](https://github.com/ktmeaton/plague-phylogeography/commit/85d16613) add slack test script
+* [```16a49470```](https://github.com/ktmeaton/plague-phylogeography/commit/16a49470) remove conda channel setup
+* [```ac9ad2a5```](https://github.com/ktmeaton/plague-phylogeography/commit/ac9ad2a5) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```c7a911b0```](https://github.com/ktmeaton/plague-phylogeography/commit/c7a911b0) make env channels consistent
+* [```a4018e12```](https://github.com/ktmeaton/plague-phylogeography/commit/a4018e12) update docs
+* [```947b1f84```](https://github.com/ktmeaton/plague-phylogeography/commit/947b1f84) Merge remote-tracking branch 'origin/master' into snakemake
+* [```4aa492d4```](https://github.com/ktmeaton/plague-phylogeography/commit/4aa492d4) add graham profile
+* [```95520ad7```](https://github.com/ktmeaton/plague-phylogeography/commit/95520ad7) fix bad sra len and report num jobs completed
+* [```88369b35```](https://github.com/ktmeaton/plague-phylogeography/commit/88369b35) remove extra python script, add start jobs log
+* [```0826c370```](https://github.com/ktmeaton/plague-phylogeography/commit/0826c370) try to set timezone
+* [```7cc3f7c4```](https://github.com/ktmeaton/plague-phylogeography/commit/7cc3f7c4) try slack logging for all rules
+* [```63c50e37```](https://github.com/ktmeaton/plague-phylogeography/commit/63c50e37) add eager to logging
+* [```786e9655```](https://github.com/ktmeaton/plague-phylogeography/commit/786e9655) test logging of first 2 runs
+* [```448ab66f```](https://github.com/ktmeaton/plague-phylogeography/commit/448ab66f) better rule logging format
+* [```6e511336```](https://github.com/ktmeaton/plague-phylogeography/commit/6e511336) reinstall bot with chat permissions
+* [```0423d4a2```](https://github.com/ktmeaton/plague-phylogeography/commit/0423d4a2) try pipeline with new token and bot
+* [```230acbb5```](https://github.com/ktmeaton/plague-phylogeography/commit/230acbb5) semi colons
+* [```e836f703```](https://github.com/ktmeaton/plague-phylogeography/commit/e836f703) try to limite nf rules to one job concurrently
+* [```20037357```](https://github.com/ktmeaton/plague-phylogeography/commit/20037357) trying download rules with slack logging
+* [```657b855d```](https://github.com/ktmeaton/plague-phylogeography/commit/657b855d) reset to one-liner
+* [```6a95ee1c```](https://github.com/ktmeaton/plague-phylogeography/commit/6a95ee1c) try creating .env file in pipeline
+* [```700620e9```](https://github.com/ktmeaton/plague-phylogeography/commit/700620e9) preparing for slack logging
+* [```67ff70fa```](https://github.com/ktmeaton/plague-phylogeography/commit/67ff70fa) run snippy multi on all 3 streams
+* [```0b2b4930```](https://github.com/ktmeaton/plague-phylogeography/commit/0b2b4930) add masking to snippy_multi
+* [```73e24140```](https://github.com/ktmeaton/plague-phylogeography/commit/73e24140) add repeat detection
+* [```be701c86```](https://github.com/ktmeaton/plague-phylogeography/commit/be701c86) sanity commit new scripts
+* [```236c202a```](https://github.com/ktmeaton/plague-phylogeography/commit/236c202a) restrict infoserv and eager resources
+* [```a2a9fba0```](https://github.com/ktmeaton/plague-phylogeography/commit/a2a9fba0) never run the update site workflow
+* [```1703ab05```](https://github.com/ktmeaton/plague-phylogeography/commit/1703ab05) test the site action chain
+* [```a8c35dbc```](https://github.com/ktmeaton/plague-phylogeography/commit/a8c35dbc) remove site from gitignore
+* [```d4053a2a```](https://github.com/ktmeaton/plague-phylogeography/commit/d4053a2a) force push new content
+* [```2b7d449e```](https://github.com/ktmeaton/plague-phylogeography/commit/2b7d449e) try pushing index to gh-pages
+* [```fea299e7```](https://github.com/ktmeaton/plague-phylogeography/commit/fea299e7) try a different way of adding front matter
+* [```e878b1be```](https://github.com/ktmeaton/plague-phylogeography/commit/e878b1be) test if adding front matter breaks things
+* [```21c76efb```](https://github.com/ktmeaton/plague-phylogeography/commit/21c76efb) test out site building workflow
+* [```f69a2a7d```](https://github.com/ktmeaton/plague-phylogeography/commit/f69a2a7d) rearrange testing cmd
+* [```a649df2c```](https://github.com/ktmeaton/plague-phylogeography/commit/a649df2c) limit docs workflow to master
+* [```5b4dd0d3```](https://github.com/ktmeaton/plague-phylogeography/commit/5b4dd0d3) test docs building again
+* [```14c657b2```](https://github.com/ktmeaton/plague-phylogeography/commit/14c657b2) limit runtime to 30 min
+* [```d6ab322c```](https://github.com/ktmeaton/plague-phylogeography/commit/d6ab322c) add link to report html
+* [```2a7a3525```](https://github.com/ktmeaton/plague-phylogeography/commit/2a7a3525) try to limit threads per rule to 2
+* [```7251a0de```](https://github.com/ktmeaton/plague-phylogeography/commit/7251a0de) simplify snippy multi filtering
+* [```0fb1d24b```](https://github.com/ktmeaton/plague-phylogeography/commit/0fb1d24b) test out using snp-sites for multi filter
+* [```55efe1a9```](https://github.com/ktmeaton/plague-phylogeography/commit/55efe1a9) multiqc edits and force log artifact
+* [```e99601f4```](https://github.com/ktmeaton/plague-phylogeography/commit/e99601f4) add multiqc testing
+* [```0ed39db4```](https://github.com/ktmeaton/plague-phylogeography/commit/0ed39db4) fix target of test snippy multi filter
+* [```1695db25```](https://github.com/ktmeaton/plague-phylogeography/commit/1695db25) add config file for multiqc
+* [```f714360b```](https://github.com/ktmeaton/plague-phylogeography/commit/f714360b) add snp-sites to iqtree env and begin qualimap
+* [```06456090```](https://github.com/ktmeaton/plague-phylogeography/commit/06456090) update test pipeline to run snippy_multi_filter separately
+* [```73ddae9b```](https://github.com/ktmeaton/plague-phylogeography/commit/73ddae9b) update descriptions and ver
+* [```a4668cda```](https://github.com/ktmeaton/plague-phylogeography/commit/a4668cda) add pre-commit to default env
+* [```d2dd9681```](https://github.com/ktmeaton/plague-phylogeography/commit/d2dd9681) try to use the fconst option
+* [```864a587f```](https://github.com/ktmeaton/plague-phylogeography/commit/864a587f) fix mixed line endings
+* [```80f71651```](https://github.com/ktmeaton/plague-phylogeography/commit/80f71651) test output snippy_multi_filter
+* [```3891688b```](https://github.com/ktmeaton/plague-phylogeography/commit/3891688b) fix dup name
+* [```666c82e6```](https://github.com/ktmeaton/plague-phylogeography/commit/666c82e6) proper max_data settings and new snippy pairwise threads
+* [```a98af3f5```](https://github.com/ktmeaton/plague-phylogeography/commit/a98af3f5) udpate profiles
+* [```474442b4```](https://github.com/ktmeaton/plague-phylogeography/commit/474442b4) add graphviz to eager
+* [```9bae116f```](https://github.com/ktmeaton/plague-phylogeography/commit/9bae116f) split up intensive test rules
+* [```47470f7e```](https://github.com/ktmeaton/plague-phylogeography/commit/47470f7e) try to limit eager mem
+* [```1d10c3e8```](https://github.com/ktmeaton/plague-phylogeography/commit/1d10c3e8) disable eager quiet log
+* [```ded90c9d```](https://github.com/ktmeaton/plague-phylogeography/commit/ded90c9d) rename cache
+* [```ace47f08```](https://github.com/ktmeaton/plague-phylogeography/commit/ace47f08) forgot to put constraints regex in quotes
+* [```09f4a2b4```](https://github.com/ktmeaton/plague-phylogeography/commit/09f4a2b4) try changing cache key to rebuild cache
+* [```8a189f29```](https://github.com/ktmeaton/plague-phylogeography/commit/8a189f29) further restrict wildcards for reads_origin
+* [```f901e4bd```](https://github.com/ktmeaton/plague-phylogeography/commit/f901e4bd) restrict ext of download_assembly
+* [```f385d8de```](https://github.com/ktmeaton/plague-phylogeography/commit/f385d8de) test the tsv method separately
+* [```6c97bdab```](https://github.com/ktmeaton/plague-phylogeography/commit/6c97bdab) add data local with new timestamp
+* [```8f1381f9```](https://github.com/ktmeaton/plague-phylogeography/commit/8f1381f9) remove bad timestamp data local
+* [```ec5b65a0```](https://github.com/ktmeaton/plague-phylogeography/commit/ec5b65a0) remove nf from default, reorganize pipeline
+* [```6fde6a7f```](https://github.com/ktmeaton/plague-phylogeography/commit/6fde6a7f) fix incorrect prefix sra to local
+* [```d5ff7b3d```](https://github.com/ktmeaton/plague-phylogeography/commit/d5ff7b3d) rearrange the order of download_sra download_assembly
+* [```e8919222```](https://github.com/ktmeaton/plague-phylogeography/commit/e8919222) new infoserve profile and channels instructions
+* [```db08fc45```](https://github.com/ktmeaton/plague-phylogeography/commit/db08fc45) minor edits to config cmd
+* [```088afe3b```](https://github.com/ktmeaton/plague-phylogeography/commit/088afe3b) clean up linting and add timeout
+* [```3caee1b3```](https://github.com/ktmeaton/plague-phylogeography/commit/3caee1b3) major update
+* [```615ea022```](https://github.com/ktmeaton/plague-phylogeography/commit/615ea022) simplify downloading rule
+* [```473f4742```](https://github.com/ktmeaton/plague-phylogeography/commit/473f4742) sanity commit before rethinking use of import
+* [```b593c7b8```](https://github.com/ktmeaton/plague-phylogeography/commit/b593c7b8) up to snippy multi with assembly
+* [```ba7ab3f8```](https://github.com/ktmeaton/plague-phylogeography/commit/ba7ab3f8) rename sqlite_import to sqlite
+* [```6fcee2fc```](https://github.com/ktmeaton/plague-phylogeography/commit/6fcee2fc) add conda one-liner
+* [```0926ce4e```](https://github.com/ktmeaton/plague-phylogeography/commit/0926ce4e) back to one-linters
+* [```5ac3fba9```](https://github.com/ktmeaton/plague-phylogeography/commit/5ac3fba9) back to one-linters
+* [```a80eac20```](https://github.com/ktmeaton/plague-phylogeography/commit/a80eac20) possibly fixed spacing
+* [```e34cd1bc```](https://github.com/ktmeaton/plague-phylogeography/commit/e34cd1bc) add eager full and download gbff and gff
+* [```b22dabf5```](https://github.com/ktmeaton/plague-phylogeography/commit/b22dabf5) mark read origin in message
+* [```72cf601d```](https://github.com/ktmeaton/plague-phylogeography/commit/72cf601d) add the eager_local tsv for testing
+* [```bdecf893```](https://github.com/ktmeaton/plague-phylogeography/commit/bdecf893) add the eager_local tsv for testing
+* [```afe9faf4```](https://github.com/ktmeaton/plague-phylogeography/commit/afe9faf4) add test_eager_local to test
+* [```ee30530c```](https://github.com/ktmeaton/plague-phylogeography/commit/ee30530c) Give report cmd a target as help
+* [```fd351cf8```](https://github.com/ktmeaton/plague-phylogeography/commit/fd351cf8) Add semicolon
+* [```d381380c```](https://github.com/ktmeaton/plague-phylogeography/commit/d381380c) wrap file input with str for help
+* [```4b6620fc```](https://github.com/ktmeaton/plague-phylogeography/commit/4b6620fc) remove nextflow pull from install setup
+* [```58437024```](https://github.com/ktmeaton/plague-phylogeography/commit/58437024) cache workflow env and try to install conda env
+* [```7d370a00```](https://github.com/ktmeaton/plague-phylogeography/commit/7d370a00) give eager all available cores
+* [```bc888a8c```](https://github.com/ktmeaton/plague-phylogeography/commit/bc888a8c) separate nf pull from create
+* [```e8d5b5c7```](https://github.com/ktmeaton/plague-phylogeography/commit/e8d5b5c7) read nf to eager env
+* [```e0f25c5c```](https://github.com/ktmeaton/plague-phylogeography/commit/e0f25c5c) forgot semi colons
+* [```ac8a1515```](https://github.com/ktmeaton/plague-phylogeography/commit/ac8a1515) move nextflow to default env
+* [```6f46ca14```](https://github.com/ktmeaton/plague-phylogeography/commit/6f46ca14) try nextflow with eager
+* [```44aa4d01```](https://github.com/ktmeaton/plague-phylogeography/commit/44aa4d01) try hashing multiple env
+* [```3c0ff5f5```](https://github.com/ktmeaton/plague-phylogeography/commit/3c0ff5f5) fix nf ver typo
+* [```c4d039cb```](https://github.com/ktmeaton/plague-phylogeography/commit/c4d039cb) rerun after local data add
+* [```891e68aa```](https://github.com/ktmeaton/plague-phylogeography/commit/891e68aa) add local testing data
+* [```233e767d```](https://github.com/ktmeaton/plague-phylogeography/commit/233e767d) add back in eager
+* [```db9b6799```](https://github.com/ktmeaton/plague-phylogeography/commit/db9b6799) successful file acc implement
+* [```b38088ef```](https://github.com/ktmeaton/plague-phylogeography/commit/b38088ef) change download dir to data
+* [```3a328656```](https://github.com/ktmeaton/plague-phylogeography/commit/3a328656) start dynamic input for eager
+* [```598d1849```](https://github.com/ktmeaton/plague-phylogeography/commit/598d1849) add quotes, fix workflow env dir
+* [```658357be```](https://github.com/ktmeaton/plague-phylogeography/commit/658357be) try a new fix in download_sra script for tokens
+* [```dbff3d10```](https://github.com/ktmeaton/plague-phylogeography/commit/dbff3d10) try to fix extra slash in path
+* [```ba22c639```](https://github.com/ktmeaton/plague-phylogeography/commit/ba22c639) fix download ref target
+* [```2c83fbe7```](https://github.com/ktmeaton/plague-phylogeography/commit/2c83fbe7) fix results_dir for download
+* [```ad7606de```](https://github.com/ktmeaton/plague-phylogeography/commit/ad7606de) add execute permission
+* [```180d8ff5```](https://github.com/ktmeaton/plague-phylogeography/commit/180d8ff5) add ending semicolons
+* [```cd09afcb```](https://github.com/ktmeaton/plague-phylogeography/commit/cd09afcb) more path fixes
+* [```69686a09```](https://github.com/ktmeaton/plague-phylogeography/commit/69686a09) more path fixes
+* [```df5bb227```](https://github.com/ktmeaton/plague-phylogeography/commit/df5bb227) fix sqlite db param
+* [```5dfede46```](https://github.com/ktmeaton/plague-phylogeography/commit/5dfede46) trying linting to ignore narratives md
+* [```3745cc82```](https://github.com/ktmeaton/plague-phylogeography/commit/3745cc82) give up on snakemake lint for now
+* [```d3a7bcf8```](https://github.com/ktmeaton/plague-phylogeography/commit/d3a7bcf8) update custom targets for testing
+* [```4fff30b3```](https://github.com/ktmeaton/plague-phylogeography/commit/4fff30b3) fix results_dir in alignment
+* [```62f5955c```](https://github.com/ktmeaton/plague-phylogeography/commit/62f5955c) add in eager to test
+* [```92229f28```](https://github.com/ktmeaton/plague-phylogeography/commit/92229f28) fix results_dir in targets
+* [```69a13438```](https://github.com/ktmeaton/plague-phylogeography/commit/69a13438) separated aggregate targets
+* [```8c96a5ad```](https://github.com/ktmeaton/plague-phylogeography/commit/8c96a5ad) update for simpler code
+* [```095c72ff```](https://github.com/ktmeaton/plague-phylogeography/commit/095c72ff) update snakemake to 5.25.0
+* [```2a151ca5```](https://github.com/ktmeaton/plague-phylogeography/commit/2a151ca5) temp working sra download
+* [```ea64551f```](https://github.com/ktmeaton/plague-phylogeography/commit/ea64551f) testing sra download
+* [```7f5d29b4```](https://github.com/ktmeaton/plague-phylogeography/commit/7f5d29b4) reinstate report as new cmd
+* [```0d2171c5```](https://github.com/ktmeaton/plague-phylogeography/commit/0d2171c5) reinstate report as new cmd
+* [```6ec6f9df```](https://github.com/ktmeaton/plague-phylogeography/commit/6ec6f9df) remove report flag
+* [```2503e213```](https://github.com/ktmeaton/plague-phylogeography/commit/2503e213) fix uses conflict
+* [```427cc01c```](https://github.com/ktmeaton/plague-phylogeography/commit/427cc01c) lint all
+* [```a49dca8c```](https://github.com/ktmeaton/plague-phylogeography/commit/a49dca8c) fix the random import
+* [```ea78d602```](https://github.com/ktmeaton/plague-phylogeography/commit/ea78d602) add tree building
+* [```f4e9d11b```](https://github.com/ktmeaton/plague-phylogeography/commit/f4e9d11b) test new pipeline workflow after updating docs
+* [```04dcd803```](https://github.com/ktmeaton/plague-phylogeography/commit/04dcd803) try run help with conda
+* [```26a6e837```](https://github.com/ktmeaton/plague-phylogeography/commit/26a6e837) update db with master table
+* [```0da96433```](https://github.com/ktmeaton/plague-phylogeography/commit/0da96433) edit desc
+* [```8c6be4e1```](https://github.com/ktmeaton/plague-phylogeography/commit/8c6be4e1) specify snippy_pairwise cores
+* [```458f45e6```](https://github.com/ktmeaton/plague-phylogeography/commit/458f45e6) add sqlite db
+* [```ae52abc7```](https://github.com/ktmeaton/plague-phylogeography/commit/ae52abc7) added gh-actions profile
+* [```6515c4b5```](https://github.com/ktmeaton/plague-phylogeography/commit/6515c4b5) test for cache hit
+* [```a8e6b725```](https://github.com/ktmeaton/plague-phylogeography/commit/a8e6b725) test for cache hit
+* [```46953e93```](https://github.com/ktmeaton/plague-phylogeography/commit/46953e93) test for cache hit
+* [```a6205bf9```](https://github.com/ktmeaton/plague-phylogeography/commit/a6205bf9) test help cmd
+* [```827d19af```](https://github.com/ktmeaton/plague-phylogeography/commit/827d19af) fix envs typo
+* [```b2a94f30```](https://github.com/ktmeaton/plague-phylogeography/commit/b2a94f30) use setup conda with mamba
+* [```41cdf8de```](https://github.com/ktmeaton/plague-phylogeography/commit/41cdf8de) test new install workflow
+* [```6cc4a310```](https://github.com/ktmeaton/plague-phylogeography/commit/6cc4a310) add first report
+* [```05185dde```](https://github.com/ktmeaton/plague-phylogeography/commit/05185dde) major nextflow cleanup
+* [```60918327```](https://github.com/ktmeaton/plague-phylogeography/commit/60918327) major nextflow cleanup
+* [```0e2b2e4a```](https://github.com/ktmeaton/plague-phylogeography/commit/0e2b2e4a) added report functionality
+* [```0ac0668e```](https://github.com/ktmeaton/plague-phylogeography/commit/0ac0668e) consolidate sample id
+* [```054e10ea```](https://github.com/ktmeaton/plague-phylogeography/commit/054e10ea) put func in sep file, figured out variable input
+* [```135b298f```](https://github.com/ktmeaton/plague-phylogeography/commit/135b298f) fix all target, now reads from db
+* [```68eb2d79```](https://github.com/ktmeaton/plague-phylogeography/commit/68eb2d79) figuring out the chain
+* [```7a7c1f9d```](https://github.com/ktmeaton/plague-phylogeography/commit/7a7c1f9d) reorganize in workflow dir
+* [```30318daf```](https://github.com/ktmeaton/plague-phylogeography/commit/30318daf) separated sqlite and download rules
+* [```6ac0dd75```](https://github.com/ktmeaton/plague-phylogeography/commit/6ac0dd75) smoothed out a downloading option
+* [```133033b3```](https://github.com/ktmeaton/plague-phylogeography/commit/133033b3) more snakemake testing
+* [```ddb90cf3```](https://github.com/ktmeaton/plague-phylogeography/commit/ddb90cf3) update docs
+* [```6d0168e9```](https://github.com/ktmeaton/plague-phylogeography/commit/6d0168e9) create rules for local reads and eager
+* [```eae2213e```](https://github.com/ktmeaton/plague-phylogeography/commit/eae2213e) first changes with snakemake
 
 ## v0.1.4
 
 ### Commits
 
-* [```b0d6107```](https://github.com/ktmeaton/plague-phylogeography/commit/b0d6107) change DB var in exhibit docs
-* [```cf23b48```](https://github.com/ktmeaton/plague-phylogeography/commit/cf23b48) update docs
-* [```7b04fc1```](https://github.com/ktmeaton/plague-phylogeography/commit/7b04fc1) add a CodeSpaces link to test
-* [```6fa9e24```](https://github.com/ktmeaton/plague-phylogeography/commit/6fa9e24) Update contributing and templates, pull docs"
-* [```5d16e3f```](https://github.com/ktmeaton/plague-phylogeography/commit/5d16e3f) update contributing and templates
-* [```5037c7d```](https://github.com/ktmeaton/plague-phylogeography/commit/5037c7d) update modern and ancient commands
-* [```2faa8e7```](https://github.com/ktmeaton/plague-phylogeography/commit/2faa8e7) update docs
-* [```c69570f```](https://github.com/ktmeaton/plague-phylogeography/commit/c69570f) Add execute to github, pull docs
-* [```af81b48```](https://github.com/ktmeaton/plague-phylogeography/commit/af81b48) add execute to github
-* [```b752a97```](https://github.com/ktmeaton/plague-phylogeography/commit/b752a97) add execute to github
-* [```2bafa86```](https://github.com/ktmeaton/plague-phylogeography/commit/2bafa86) update docs
-* [```81a4e4e```](https://github.com/ktmeaton/plague-phylogeography/commit/81a4e4e) generic loci extract, pull docs
-* [```e558a03```](https://github.com/ktmeaton/plague-phylogeography/commit/e558a03) remove param sqlite
-* [```3837061```](https://github.com/ktmeaton/plague-phylogeography/commit/3837061) tackled some high and low priorities
-* [```d4c8bfa```](https://github.com/ktmeaton/plague-phylogeography/commit/d4c8bfa) update ncbimeta params
-* [```44d0b95```](https://github.com/ktmeaton/plague-phylogeography/commit/44d0b95) allow generic locus extraction
-* [```1988026```](https://github.com/ktmeaton/plague-phylogeography/commit/1988026) change from split to generic extract
-* [```1caa43c```](https://github.com/ktmeaton/plague-phylogeography/commit/1caa43c) change ref genome add locus info
-* [```3305261```](https://github.com/ktmeaton/plague-phylogeography/commit/3305261) update docs
-* [```fc47ea9```](https://github.com/ktmeaton/plague-phylogeography/commit/fc47ea9) Change local to custom, pull docs
-* [```64ebbab```](https://github.com/ktmeaton/plague-phylogeography/commit/64ebbab) change custom to local
-* [```563671e```](https://github.com/ktmeaton/plague-phylogeography/commit/563671e) update docs
-* [```22b0577```](https://github.com/ktmeaton/plague-phylogeography/commit/22b0577) fix pipeline var typo
-* [```02a9237```](https://github.com/ktmeaton/plague-phylogeography/commit/02a9237) fix goofy sql escape char
-* [```e3cf4cb```](https://github.com/ktmeaton/plague-phylogeography/commit/e3cf4cb) change custom dir to example
-* [```1c4bb3d```](https://github.com/ktmeaton/plague-phylogeography/commit/1c4bb3d) test relative paths and merge docs
-* [```582a4ed```](https://github.com/ktmeaton/plague-phylogeography/commit/582a4ed) try workflows with relative paths
-* [```3e4189c```](https://github.com/ktmeaton/plague-phylogeography/commit/3e4189c) update docs
-* [```7c1e065```](https://github.com/ktmeaton/plague-phylogeography/commit/7c1e065) proper channel support for ncbimeta_annot
-* [```87440bb```](https://github.com/ktmeaton/plague-phylogeography/commit/87440bb) fix indentation
-* [```fd26b5a```](https://github.com/ktmeaton/plague-phylogeography/commit/fd26b5a) update workflow job name
-* [```a9156a0```](https://github.com/ktmeaton/plague-phylogeography/commit/a9156a0) add biosample backup tsv
-* [```1e10522```](https://github.com/ktmeaton/plague-phylogeography/commit/1e10522) add echo true to ncbimeta processes and eager
-* [```a6b9605```](https://github.com/ktmeaton/plague-phylogeography/commit/a6b9605) add proper slash and test db path
-* [```448100f```](https://github.com/ktmeaton/plague-phylogeography/commit/448100f) add proper slash and test db path
-* [```0643b18```](https://github.com/ktmeaton/plague-phylogeography/commit/0643b18) check pwd
-* [```80829dc```](https://github.com/ktmeaton/plague-phylogeography/commit/80829dc) remove bad Biosample_id column
-* [```e0fa222```](https://github.com/ktmeaton/plague-phylogeography/commit/e0fa222) get path for test db
-* [```61938fe```](https://github.com/ktmeaton/plague-phylogeography/commit/61938fe) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```13b13e6```](https://github.com/ktmeaton/plague-phylogeography/commit/13b13e6) extend runtime and use resume
-* [```d9a1a6f```](https://github.com/ktmeaton/plague-phylogeography/commit/d9a1a6f) update docs
-* [```2e19878```](https://github.com/ktmeaton/plague-phylogeography/commit/2e19878) attempt to put api param in quotes
-* [```a82ca7c```](https://github.com/ktmeaton/plague-phylogeography/commit/a82ca7c) remove sed replacment from config file
-* [```a16ef0a```](https://github.com/ktmeaton/plague-phylogeography/commit/a16ef0a) enforce black ver
-* [```8646c0b```](https://github.com/ktmeaton/plague-phylogeography/commit/8646c0b) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```c87e885```](https://github.com/ktmeaton/plague-phylogeography/commit/c87e885) test pipeline db after ncbimeta 0.7.0 release
-* [```dc6b859```](https://github.com/ktmeaton/plague-phylogeography/commit/dc6b859) update docs
-* [```07b553c```](https://github.com/ktmeaton/plague-phylogeography/commit/07b553c) test workflows for ncbimeta v0.7.0
-* [```5ca2480```](https://github.com/ktmeaton/plague-phylogeography/commit/5ca2480) try workflow after restricting biopython
-* [```30a047d```](https://github.com/ktmeaton/plague-phylogeography/commit/30a047d) restrict biopython to 1.74
-* [```7219e2d```](https://github.com/ktmeaton/plague-phylogeography/commit/7219e2d) make note of biopython restriction
-* [```642d6a5```](https://github.com/ktmeaton/plague-phylogeography/commit/642d6a5) try to customize db yaml
-* [```1005284```](https://github.com/ktmeaton/plague-phylogeography/commit/1005284) recome sqlite param from db create
-* [```b55f2fa```](https://github.com/ktmeaton/plague-phylogeography/commit/b55f2fa) note to troubleshoot ncbimeta error
-* [```e141021```](https://github.com/ktmeaton/plague-phylogeography/commit/e141021) add python 3.7 to conda env
-* [```4e422be```](https://github.com/ktmeaton/plague-phylogeography/commit/4e422be) use relative path for custom reads
-* [```99bf05c```](https://github.com/ktmeaton/plague-phylogeography/commit/99bf05c) remove nextstrain uninstall
-* [```930e2bc```](https://github.com/ktmeaton/plague-phylogeography/commit/930e2bc) remove nextrain env cache
-* [```ee905fb```](https://github.com/ktmeaton/plague-phylogeography/commit/ee905fb) try using the var HOME for custom tsv
-* [```7b5c9ff```](https://github.com/ktmeaton/plague-phylogeography/commit/7b5c9ff) fix double tsv file input for eager
-* [```723d32e```](https://github.com/ktmeaton/plague-phylogeography/commit/723d32e) add linting notes and process docs
-* [```21be21c```](https://github.com/ktmeaton/plague-phylogeography/commit/21be21c) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```a7e2c45```](https://github.com/ktmeaton/plague-phylogeography/commit/a7e2c45) test doc workflow when no file changes
-* [```6ce2b20```](https://github.com/ktmeaton/plague-phylogeography/commit/6ce2b20) update docs
-* [```e46d58e```](https://github.com/ktmeaton/plague-phylogeography/commit/e46d58e) try separating push
-* [```157b2c7```](https://github.com/ktmeaton/plague-phylogeography/commit/157b2c7) try or statements for commit and push
-* [```7e452ad```](https://github.com/ktmeaton/plague-phylogeography/commit/7e452ad) add debugging statement
-* [```94a0a03```](https://github.com/ktmeaton/plague-phylogeography/commit/94a0a03) try deleting untrack files again
-* [```fcfed03```](https://github.com/ktmeaton/plague-phylogeography/commit/fcfed03) try deleting untrack files again
-* [```9c05487```](https://github.com/ktmeaton/plague-phylogeography/commit/9c05487) update docs process_all
-* [```ab8aaba```](https://github.com/ktmeaton/plague-phylogeography/commit/ab8aaba) escape wildcard characters
-* [```027d098```](https://github.com/ktmeaton/plague-phylogeography/commit/027d098) test upload process_all
-* [```97e262b```](https://github.com/ktmeaton/plague-phylogeography/commit/97e262b) remove old process docs
-* [```14763ac```](https://github.com/ktmeaton/plague-phylogeography/commit/14763ac) test untracking auto docs
-* [```0d7763d```](https://github.com/ktmeaton/plague-phylogeography/commit/0d7763d) update docs process_all
-* [```484b749```](https://github.com/ktmeaton/plague-phylogeography/commit/484b749) use section text in main and process_docs
-* [```dccdfb9```](https://github.com/ktmeaton/plague-phylogeography/commit/dccdfb9) commit updated process_all if changed
-* [```ad119db```](https://github.com/ktmeaton/plague-phylogeography/commit/ad119db) docs workflow depends on process_docs script
-* [```a68cab7```](https://github.com/ktmeaton/plague-phylogeography/commit/a68cab7) run python linter
-* [```c9ff182```](https://github.com/ktmeaton/plague-phylogeography/commit/c9ff182) test linter
-* [```2403546```](https://github.com/ktmeaton/plague-phylogeography/commit/2403546) test linter
-* [```7ddcfde```](https://github.com/ktmeaton/plague-phylogeography/commit/7ddcfde) workflow creates process_all from docstrings
-* [```eaefcdf```](https://github.com/ktmeaton/plague-phylogeography/commit/eaefcdf) auto docstring build
-* [```aff27f4```](https://github.com/ktmeaton/plague-phylogeography/commit/aff27f4) add process docs script
-* [```079a115```](https://github.com/ktmeaton/plague-phylogeography/commit/079a115) restore no channel specify, remove excess docs
-* [```26da567```](https://github.com/ktmeaton/plague-phylogeography/commit/26da567) re-add conda forge channel
-* [```08928d5```](https://github.com/ktmeaton/plague-phylogeography/commit/08928d5) don't install nextstrain env
-* [```b20299b```](https://github.com/ktmeaton/plague-phylogeography/commit/b20299b) don't install nextstrain env
-* [```cd5b0a9```](https://github.com/ktmeaton/plague-phylogeography/commit/cd5b0a9) don't install nextstrain env
-* [```137b258```](https://github.com/ktmeaton/plague-phylogeography/commit/137b258) try removing conda-forge from phylo env
-* [```7ae5af5```](https://github.com/ktmeaton/plague-phylogeography/commit/7ae5af5) change local tsv to nf paths
-* [```7dc4822```](https://github.com/ktmeaton/plague-phylogeography/commit/7dc4822) change local tsv to nf paths
-* [```b32736c```](https://github.com/ktmeaton/plague-phylogeography/commit/b32736c) fix sqlite db repo var
-* [```9e41768```](https://github.com/ktmeaton/plague-phylogeography/commit/9e41768) change github repo and sha var
-* [```2d377d5```](https://github.com/ktmeaton/plague-phylogeography/commit/2d377d5) test the db pipeline
-* [```ab3d7ba```](https://github.com/ktmeaton/plague-phylogeography/commit/ab3d7ba) Merge in new README
-* [```6fa92da```](https://github.com/ktmeaton/plague-phylogeography/commit/6fa92da) retry github repo var
-* [```4ba5ba1```](https://github.com/ktmeaton/plague-phylogeography/commit/4ba5ba1) update docs README
-* [```33e47b5```](https://github.com/ktmeaton/plague-phylogeography/commit/33e47b5) link point to nf path rather than local
-* [```723558e```](https://github.com/ktmeaton/plague-phylogeography/commit/723558e) now testing ncbimeta update v0.6.6
-* [```fd3b6a3```](https://github.com/ktmeaton/plague-phylogeography/commit/fd3b6a3) update install script to use repo and sha
-* [```a006df2```](https://github.com/ktmeaton/plague-phylogeography/commit/a006df2) fix conda update input
-* [```433088c```](https://github.com/ktmeaton/plague-phylogeography/commit/433088c) test ncbimeta 0.6.6 and auto update conda
-* [```f53e0dc```](https://github.com/ktmeaton/plague-phylogeography/commit/f53e0dc) remove debug and test load cache
-* [```95b6028```](https://github.com/ktmeaton/plague-phylogeography/commit/95b6028) backup manual annotations
-* [```c64caf3```](https://github.com/ktmeaton/plague-phylogeography/commit/c64caf3) search for conda.sh in home or usr share
-* [```efe9a65```](https://github.com/ktmeaton/plague-phylogeography/commit/efe9a65) search for conda.sh in home or usr share
-* [```9b8f8cb```](https://github.com/ktmeaton/plague-phylogeography/commit/9b8f8cb) test conda exe location
-* [```85750db```](https://github.com/ktmeaton/plague-phylogeography/commit/85750db) inspect profile.d dir
-* [```6480e39```](https://github.com/ktmeaton/plague-phylogeography/commit/6480e39) more debug to check usr share path
-* [```5754fb3```](https://github.com/ktmeaton/plague-phylogeography/commit/5754fb3) extra debug statements to check cache
-* [```7fa5de1```](https://github.com/ktmeaton/plague-phylogeography/commit/7fa5de1) retry install with longer runtime
-* [```ce23bf6```](https://github.com/ktmeaton/plague-phylogeography/commit/ce23bf6) specify repo and sha with install script
-* [```fa318c5```](https://github.com/ktmeaton/plague-phylogeography/commit/fa318c5) update with env name
-* [```88995fe```](https://github.com/ktmeaton/plague-phylogeography/commit/88995fe) fix header lint spacing
-* [```72a5bcd```](https://github.com/ktmeaton/plague-phylogeography/commit/72a5bcd) update 0.1.4 changes and to do
-* [```5067615```](https://github.com/ktmeaton/plague-phylogeography/commit/5067615) ignore sra dir
-* [```62e00c9```](https://github.com/ktmeaton/plague-phylogeography/commit/62e00c9) try local data pipeline
-* [```a8b1514```](https://github.com/ktmeaton/plague-phylogeography/commit/a8b1514) more flexible tsv naming
-* [```414c07b```](https://github.com/ktmeaton/plague-phylogeography/commit/414c07b) attempt more local reads to avoid 0 SNP call
-* [```730161a```](https://github.com/ktmeaton/plague-phylogeography/commit/730161a) more flexible custom tsv naming
-* [```23d6ba3```](https://github.com/ktmeaton/plague-phylogeography/commit/23d6ba3) allow local reads and assemblies
-* [```e34842e```](https://github.com/ktmeaton/plague-phylogeography/commit/e34842e) add java install notes
-* [```f897478```](https://github.com/ktmeaton/plague-phylogeography/commit/f897478) add new to do
-* [```5788318```](https://github.com/ktmeaton/plague-phylogeography/commit/5788318) comment to explain check max vals
-* [```e5c3344```](https://github.com/ktmeaton/plague-phylogeography/commit/e5c3344) remove combine pipeline
-* [```eb6aace```](https://github.com/ktmeaton/plague-phylogeography/commit/eb6aace) reset check max time
-* [```264df9f```](https://github.com/ktmeaton/plague-phylogeography/commit/264df9f) begin commenting low coverage EAGER Ancient
-* [```37281bc```](https://github.com/ktmeaton/plague-phylogeography/commit/37281bc) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```52454a3```](https://github.com/ktmeaton/plague-phylogeography/commit/52454a3) add mv statement
-* [```1dfd7cf```](https://github.com/ktmeaton/plague-phylogeography/commit/1dfd7cf) update docs README
-* [```5542e3c```](https://github.com/ktmeaton/plague-phylogeography/commit/5542e3c) move eager output of multiqc and pipeline_info
-* [```f8f5387```](https://github.com/ktmeaton/plague-phylogeography/commit/f8f5387) add conda links
-* [```eceaebe```](https://github.com/ktmeaton/plague-phylogeography/commit/eceaebe) sanity commit
-* [```ee4a33e```](https://github.com/ktmeaton/plague-phylogeography/commit/ee4a33e) lower timeouts back down ot 30 min
-* [```f94d823```](https://github.com/ktmeaton/plague-phylogeography/commit/f94d823) limit iqtree threads, remove bnni param
-* [```275563f```](https://github.com/ktmeaton/plague-phylogeography/commit/275563f) try extending runtime limit
-* [```dddb53e```](https://github.com/ktmeaton/plague-phylogeography/commit/dddb53e) add proper gh resources
-* [```166532f```](https://github.com/ktmeaton/plague-phylogeography/commit/166532f) fix bam readgroup error snippy
-* [```6cd5a8e```](https://github.com/ktmeaton/plague-phylogeography/commit/6cd5a8e) change output of eager to the lib merged bam
-* [```c50013c```](https://github.com/ktmeaton/plague-phylogeography/commit/c50013c) rearrange sra config settings
-* [```fcb3481```](https://github.com/ktmeaton/plague-phylogeography/commit/fcb3481) try new workflow with combine
-* [```e27d08d```](https://github.com/ktmeaton/plague-phylogeography/commit/e27d08d) add trace info to docs
-* [```2b0543f```](https://github.com/ktmeaton/plague-phylogeography/commit/2b0543f) if sra cache is already set, retrieve it
-* [```ab96ecb```](https://github.com/ktmeaton/plague-phylogeography/commit/ab96ecb) add dev to ver number
-* [```66671d6```](https://github.com/ktmeaton/plague-phylogeography/commit/66671d6) keep outdir consistent so caching works
-* [```8f440ac```](https://github.com/ktmeaton/plague-phylogeography/commit/8f440ac) update modern and ancient docs
-* [```5982d09```](https://github.com/ktmeaton/plague-phylogeography/commit/5982d09) Testing sra validate and metadata linking
-* [```863d0df```](https://github.com/ktmeaton/plague-phylogeography/commit/863d0df) validate sra download, add biosample acc to path
-* [```7248e29```](https://github.com/ktmeaton/plague-phylogeography/commit/7248e29) add biosample acc to fastq path
-* [```a1f0515```](https://github.com/ktmeaton/plague-phylogeography/commit/a1f0515) update docs README
-* [```1099d02```](https://github.com/ktmeaton/plague-phylogeography/commit/1099d02) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```2db7ec5```](https://github.com/ktmeaton/plague-phylogeography/commit/2db7ec5) fix credits spacing
-* [```f51e071```](https://github.com/ktmeaton/plague-phylogeography/commit/f51e071) test iqtree model param
-* [```321419b```](https://github.com/ktmeaton/plague-phylogeography/commit/321419b) allow sra path to run parallel for biosample, add model param to iqtree
-* [```09326d2```](https://github.com/ktmeaton/plague-phylogeography/commit/09326d2) change sra metadata to biosample, add iqtree model param, fix time default max
-* [```b224464```](https://github.com/ktmeaton/plague-phylogeography/commit/b224464) update docs README
-* [```7cea6fe```](https://github.com/ktmeaton/plague-phylogeography/commit/7cea6fe) further reduce timeout to 60 min
-* [```61fb587```](https://github.com/ktmeaton/plague-phylogeography/commit/61fb587) constraint maxForks to specified maxForks
-* [```1a8a74e```](https://github.com/ktmeaton/plague-phylogeography/commit/1a8a74e) new terminal output for v0.1.4
-* [```487ec9e```](https://github.com/ktmeaton/plague-phylogeography/commit/487ec9e) reoptimize for parallel cluster
-* [```012c1d9```](https://github.com/ktmeaton/plague-phylogeography/commit/012c1d9) fix tag for snippy_pairwise
-* [```63b9611```](https://github.com/ktmeaton/plague-phylogeography/commit/63b9611) load all caches for compatibility with install script
-* [```602f7ca```](https://github.com/ktmeaton/plague-phylogeography/commit/602f7ca) try sra with new install script
-* [```f742a39```](https://github.com/ktmeaton/plague-phylogeography/commit/f742a39) remove references to step id
-* [```3db5713```](https://github.com/ktmeaton/plague-phylogeography/commit/3db5713) test assembly with new install script
-* [```8cbc9ae```](https://github.com/ktmeaton/plague-phylogeography/commit/8cbc9ae) add check cache
-* [```3185aeb```](https://github.com/ktmeaton/plague-phylogeography/commit/3185aeb) consolidate test env step
-* [```1622567```](https://github.com/ktmeaton/plague-phylogeography/commit/1622567) don't depend on install script
-* [```b8245fa```](https://github.com/ktmeaton/plague-phylogeography/commit/b8245fa) try install workflow with simplified script
-* [```71bed77```](https://github.com/ktmeaton/plague-phylogeography/commit/71bed77) check conda env before trying to create
-* [```0315666```](https://github.com/ktmeaton/plague-phylogeography/commit/0315666) conda env checking before uninstall
-* [```85a57fd```](https://github.com/ktmeaton/plague-phylogeography/commit/85a57fd) fix REPO capitals
-* [```6db86a2```](https://github.com/ktmeaton/plague-phylogeography/commit/6db86a2) fix bad command if check
-* [```a3b8d33```](https://github.com/ktmeaton/plague-phylogeography/commit/a3b8d33) use file check rather than ls
-* [```e618979```](https://github.com/ktmeaton/plague-phylogeography/commit/e618979) try catch for uninstalled files
-* [```e2128d5```](https://github.com/ktmeaton/plague-phylogeography/commit/e2128d5) better placed env var
-* [```1039498```](https://github.com/ktmeaton/plague-phylogeography/commit/1039498) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```b382795```](https://github.com/ktmeaton/plague-phylogeography/commit/b382795) better env catch and make uninstall generic
-* [```20394da```](https://github.com/ktmeaton/plague-phylogeography/commit/20394da) update docs README
-* [```517d268```](https://github.com/ktmeaton/plague-phylogeography/commit/517d268) Merge assembly missing data typo change
-* [```0d1a9ea```](https://github.com/ktmeaton/plague-phylogeography/commit/0d1a9ea) make install more generic
-* [```4fb5195```](https://github.com/ktmeaton/plague-phylogeography/commit/4fb5195) Fix typo in missing data
-* [```dadff42```](https://github.com/ktmeaton/plague-phylogeography/commit/dadff42) update docs README
-* [```131c26a```](https://github.com/ktmeaton/plague-phylogeography/commit/131c26a) simplify install instructions
-* [```671ecc3```](https://github.com/ktmeaton/plague-phylogeography/commit/671ecc3) try out missing data
-* [```665690e```](https://github.com/ktmeaton/plague-phylogeography/commit/665690e) update steps and exec mode
-* [```027b287```](https://github.com/ktmeaton/plague-phylogeography/commit/027b287) typo consistency
-* [```692633c```](https://github.com/ktmeaton/plague-phylogeography/commit/692633c) test run support and independent runs
-* [```40274ed```](https://github.com/ktmeaton/plague-phylogeography/commit/40274ed) add new optional iqtree output for support and runs
-* [```90aa13f```](https://github.com/ktmeaton/plague-phylogeography/commit/90aa13f) shorten timeout
-* [```a2aa94f```](https://github.com/ktmeaton/plague-phylogeography/commit/a2aa94f) add install and uninstall scripts
-* [```bdc6909```](https://github.com/ktmeaton/plague-phylogeography/commit/bdc6909) remove for_ prefix
-* [```cd2113e```](https://github.com/ktmeaton/plague-phylogeography/commit/cd2113e) update docstrings remove unnecessary for_ prefix
-* [```ec7386d```](https://github.com/ktmeaton/plague-phylogeography/commit/ec7386d) remove jackknifing
-* [```e074b7d```](https://github.com/ktmeaton/plague-phylogeography/commit/e074b7d) try 3 datasets instead of 4
-* [```9f73566```](https://github.com/ktmeaton/plague-phylogeography/commit/9f73566) add failsafe dataset limiter
-* [```543c249```](https://github.com/ktmeaton/plague-phylogeography/commit/543c249) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```19adaf9```](https://github.com/ktmeaton/plague-phylogeography/commit/19adaf9) remove debug echo statements
-* [```17acddf```](https://github.com/ktmeaton/plague-phylogeography/commit/17acddf) update docs README
-* [```2a46bfe```](https://github.com/ktmeaton/plague-phylogeography/commit/2a46bfe) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```f095053```](https://github.com/ktmeaton/plague-phylogeography/commit/f095053) reinstate update check
-* [```ce88dc6```](https://github.com/ktmeaton/plague-phylogeography/commit/ce88dc6) update docs README
-* [```3de043c```](https://github.com/ktmeaton/plague-phylogeography/commit/3de043c) debug echo statements
-* [```dc9e96f```](https://github.com/ktmeaton/plague-phylogeography/commit/dc9e96f) update conda install and eager install
-* [```c845923```](https://github.com/ktmeaton/plague-phylogeography/commit/c845923) test getting readme update
-* [```2d36f5a```](https://github.com/ktmeaton/plague-phylogeography/commit/2d36f5a) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```e6148f6```](https://github.com/ktmeaton/plague-phylogeography/commit/e6148f6) rerun pipelines with new cache names
-* [```427d1ed```](https://github.com/ktmeaton/plague-phylogeography/commit/427d1ed) hide toc make readme home page
-* [```ab9955e```](https://github.com/ktmeaton/plague-phylogeography/commit/ab9955e) update docs README
-* [```24c1db3```](https://github.com/ktmeaton/plague-phylogeography/commit/24c1db3) force commiting and pushing
-* [```86eee3b```](https://github.com/ktmeaton/plague-phylogeography/commit/86eee3b) don't check for file update
-* [```25bc66a```](https://github.com/ktmeaton/plague-phylogeography/commit/25bc66a) put update output in if statement
-* [```bdcedfa```](https://github.com/ktmeaton/plague-phylogeography/commit/bdcedfa) rebuild env cache with new names
-* [```b08b706```](https://github.com/ktmeaton/plague-phylogeography/commit/b08b706) remove wrong markdown README
-* [```1f00571```](https://github.com/ktmeaton/plague-phylogeography/commit/1f00571) remove wrong markdown README
-* [```7974751```](https://github.com/ktmeaton/plague-phylogeography/commit/7974751) test skipping outgroup download
-* [```e2c6a49```](https://github.com/ktmeaton/plague-phylogeography/commit/e2c6a49) only commit readme if updated
-* [```73a8aab```](https://github.com/ktmeaton/plague-phylogeography/commit/73a8aab) force adding the docs README
-* [```b569b70```](https://github.com/ktmeaton/plague-phylogeography/commit/b569b70) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```db7ed4d```](https://github.com/ktmeaton/plague-phylogeography/commit/db7ed4d) ignore docs/README.rst
-* [```35a2222```](https://github.com/ktmeaton/plague-phylogeography/commit/35a2222) try not wrapping mem in single quotes
-* [```5aae865```](https://github.com/ktmeaton/plague-phylogeography/commit/5aae865) fix artifact name
-* [```6b9191f```](https://github.com/ktmeaton/plague-phylogeography/commit/6b9191f) update docs README
-* [```5588990```](https://github.com/ktmeaton/plague-phylogeography/commit/5588990) test pushing new README
-* [```159c0be```](https://github.com/ktmeaton/plague-phylogeography/commit/159c0be) move README.rst into docs folder
-* [```29a99ef```](https://github.com/ktmeaton/plague-phylogeography/commit/29a99ef) disable multiple runs temp
-* [```a61140c```](https://github.com/ktmeaton/plague-phylogeography/commit/a61140c) disable multiple runs temp
-* [```c7ae27f```](https://github.com/ktmeaton/plague-phylogeography/commit/c7ae27f) reformat docs and linting to organize
-* [```f872cd4```](https://github.com/ktmeaton/plague-phylogeography/commit/f872cd4) rename cache restore id
-* [```42331f8```](https://github.com/ktmeaton/plague-phylogeography/commit/42331f8) add resume to the longTest
-* [```14ab311```](https://github.com/ktmeaton/plague-phylogeography/commit/14ab311) add 2 hour timeout limit
-* [```68a0f94```](https://github.com/ktmeaton/plague-phylogeography/commit/68a0f94) force 30 min timeout
-* [```ae9e0e3```](https://github.com/ktmeaton/plague-phylogeography/commit/ae9e0e3) add a long test and change artifacts to long
-* [```27cd6c8```](https://github.com/ktmeaton/plague-phylogeography/commit/27cd6c8) remove hardcode repository name
-* [```9803084```](https://github.com/ktmeaton/plague-phylogeography/commit/9803084) add back in the conda env var
-* [```b3ce4ef```](https://github.com/ktmeaton/plague-phylogeography/commit/b3ce4ef) fix conditional path
-* [```8987241```](https://github.com/ktmeaton/plague-phylogeography/commit/8987241) use github sha and proper hash
-* [```b6d53fa```](https://github.com/ktmeaton/plague-phylogeography/commit/b6d53fa) check conda env and fix hash file
-* [```f117569```](https://github.com/ktmeaton/plague-phylogeography/commit/f117569) split workflows, fail assembly if cache not restored
-* [```c1c102b```](https://github.com/ktmeaton/plague-phylogeography/commit/c1c102b) change cache restore step id
-* [```9b9aaff```](https://github.com/ktmeaton/plague-phylogeography/commit/9b9aaff) add conda cache restore to assembly pipeline
-* [```280abf5```](https://github.com/ktmeaton/plague-phylogeography/commit/280abf5) fix typo and add artifacts
-* [```55fca10```](https://github.com/ktmeaton/plague-phylogeography/commit/55fca10) add conda setup
-* [```c31f40c```](https://github.com/ktmeaton/plague-phylogeography/commit/c31f40c) add assembly pipeline to cache test
-* [```abd5271```](https://github.com/ktmeaton/plague-phylogeography/commit/abd5271) test global install again
-* [```3ab19df```](https://github.com/ktmeaton/plague-phylogeography/commit/3ab19df) add the conda env paths
-* [```17c2042```](https://github.com/ktmeaton/plague-phylogeography/commit/17c2042) incorporate plague-phylo cache
-* [```7646440```](https://github.com/ktmeaton/plague-phylogeography/commit/7646440) echo statements to test nextstrain
-* [```13b70a4```](https://github.com/ktmeaton/plague-phylogeography/commit/13b70a4) add env var for phylo and nextstrain
-* [```c739960```](https://github.com/ktmeaton/plague-phylogeography/commit/c739960) don't install auspice globally
-* [```52fa974```](https://github.com/ktmeaton/plague-phylogeography/commit/52fa974) test load and add nextstrain install
-* [```d25698c```](https://github.com/ktmeaton/plague-phylogeography/commit/d25698c) fix nextflow channel and add phylo install and test
-* [```12239d5```](https://github.com/ktmeaton/plague-phylogeography/commit/12239d5) add downloading phylo pipeline
-* [```364870f```](https://github.com/ktmeaton/plague-phylogeography/commit/364870f) version match eager nf
-* [```9595d58```](https://github.com/ktmeaton/plague-phylogeography/commit/9595d58) test loading eager env cache
-* [```23b5bbb```](https://github.com/ktmeaton/plague-phylogeography/commit/23b5bbb) move eager env file to github workspace
-* [```3b3e77f```](https://github.com/ktmeaton/plague-phylogeography/commit/3b3e77f) use an absolute path for hashfiles env
-* [```0ad7635```](https://github.com/ktmeaton/plague-phylogeography/commit/0ad7635) test cache eager env
-* [```ab082d9```](https://github.com/ktmeaton/plague-phylogeography/commit/ab082d9) add cache-test id
-* [```2b0eb18```](https://github.com/ktmeaton/plague-phylogeography/commit/2b0eb18) don't create or install if cache hit
-* [```ef4789b```](https://github.com/ktmeaton/plague-phylogeography/commit/ef4789b) check test env pre
-* [```86237ca```](https://github.com/ktmeaton/plague-phylogeography/commit/86237ca) retry cache load
-* [```d859530```](https://github.com/ktmeaton/plague-phylogeography/commit/d859530) try to load env cache without exclude dir
-* [```1741ebd```](https://github.com/ktmeaton/plague-phylogeography/commit/1741ebd) try to load env cache
-* [```40ecb62```](https://github.com/ktmeaton/plague-phylogeography/commit/40ecb62) try to cache env rather than pkgs
-* [```5cbc365```](https://github.com/ktmeaton/plague-phylogeography/commit/5cbc365) make conda envs path a global var
-* [```889d18b```](https://github.com/ktmeaton/plague-phylogeography/commit/889d18b) change env path after setup
-* [```82425bd```](https://github.com/ktmeaton/plague-phylogeography/commit/82425bd) change env path before setup
-* [```4dc71ef```](https://github.com/ktmeaton/plague-phylogeography/commit/4dc71ef) check env location
-* [```70747a2```](https://github.com/ktmeaton/plague-phylogeography/commit/70747a2) try to load cache
-* [```4935db4```](https://github.com/ktmeaton/plague-phylogeography/commit/4935db4) hardcode conda path
-* [```cbe22a8```](https://github.com/ktmeaton/plague-phylogeography/commit/cbe22a8) try conda path as var
-* [```e26d281```](https://github.com/ktmeaton/plague-phylogeography/commit/e26d281) test2 with local cache dir
-* [```d7a1779```](https://github.com/ktmeaton/plague-phylogeography/commit/d7a1779) minimal test env
-* [```ea47cb7```](https://github.com/ktmeaton/plague-phylogeography/commit/ea47cb7) try to cache after conda setup
-* [```625dc7e```](https://github.com/ktmeaton/plague-phylogeography/commit/625dc7e) now test if cache loads
-* [```b503cfa```](https://github.com/ktmeaton/plague-phylogeography/commit/b503cfa) checkout repo to get hash env
-* [```0147a4d```](https://github.com/ktmeaton/plague-phylogeography/commit/0147a4d) hash env file into cache name
-* [```f3a28a5```](https://github.com/ktmeaton/plague-phylogeography/commit/f3a28a5) hash env file into cache name
-* [```11a8ffc```](https://github.com/ktmeaton/plague-phylogeography/commit/11a8ffc) better cache name
-* [```f482e9b```](https://github.com/ktmeaton/plague-phylogeography/commit/f482e9b) test caching
-* [```93e9734```](https://github.com/ktmeaton/plague-phylogeography/commit/93e9734) test plain without cache
-* [```78f12de```](https://github.com/ktmeaton/plague-phylogeography/commit/78f12de) stop before snippy multi
-* [```8d56c80```](https://github.com/ktmeaton/plague-phylogeography/commit/8d56c80) add env links
-* [```d45b13b```](https://github.com/ktmeaton/plague-phylogeography/commit/d45b13b) attempt npm cache
-* [```ee33c6f```](https://github.com/ktmeaton/plague-phylogeography/commit/ee33c6f) fix param line end typo
-* [```434a210```](https://github.com/ktmeaton/plague-phylogeography/commit/434a210) add full pipeline
-* [```67002d9```](https://github.com/ktmeaton/plague-phylogeography/commit/67002d9) update description
-* [```18809cd```](https://github.com/ktmeaton/plague-phylogeography/commit/18809cd) add alrt and jackknife to branch support opt
-* [```5ea5c16```](https://github.com/ktmeaton/plague-phylogeography/commit/5ea5c16) update artifact paths
-* [```ba5dd5e```](https://github.com/ktmeaton/plague-phylogeography/commit/ba5dd5e) update artifact paths
-* [```345852b```](https://github.com/ktmeaton/plague-phylogeography/commit/345852b) troubleshoot missing artifact paths
-* [```c63cadc```](https://github.com/ktmeaton/plague-phylogeography/commit/c63cadc) fix param typos in eager process
-* [```77d3cd0```](https://github.com/ktmeaton/plague-phylogeography/commit/77d3cd0) run everything max resources param
-* [```5d3dc45```](https://github.com/ktmeaton/plague-phylogeography/commit/5d3dc45) test echo of dedupbam
-* [```379943b```](https://github.com/ktmeaton/plague-phylogeography/commit/379943b) test ls of dedupbam
-* [```3b2a397```](https://github.com/ktmeaton/plague-phylogeography/commit/3b2a397) comment out dedup rename
-* [```90daac8```](https://github.com/ktmeaton/plague-phylogeography/commit/90daac8) test eager cmd with dedup rename
-* [```09b9caa```](https://github.com/ktmeaton/plague-phylogeography/commit/09b9caa) upload conda export as artifact
-* [```759a9c4```](https://github.com/ktmeaton/plague-phylogeography/commit/759a9c4) add a conda list export each activate
-* [```f5303af```](https://github.com/ktmeaton/plague-phylogeography/commit/f5303af) try sra workflow as phylo cmd
-* [```a37465b```](https://github.com/ktmeaton/plague-phylogeography/commit/a37465b) parameterize eager var
-* [```6f2fc88```](https://github.com/ktmeaton/plague-phylogeography/commit/6f2fc88) revert back to plain eager test cmd
-* [```806c583```](https://github.com/ktmeaton/plague-phylogeography/commit/806c583) add proper conda activate
-* [```4ec5ed2```](https://github.com/ktmeaton/plague-phylogeography/commit/4ec5ed2) try vt install with 2015 label ver
-* [```c6636e9```](https://github.com/ktmeaton/plague-phylogeography/commit/c6636e9) install workflow won't depend on main pipeline
-* [```0255718```](https://github.com/ktmeaton/plague-phylogeography/commit/0255718) reinstate snippy command and remove reference dir output
-* [```a14a4ca```](https://github.com/ktmeaton/plague-phylogeography/commit/a14a4ca) vt before snippy install
-* [```140bd07```](https://github.com/ktmeaton/plague-phylogeography/commit/140bd07) fix broken vt dependncy to 0.57721
-* [```988d9ed```](https://github.com/ktmeaton/plague-phylogeography/commit/988d9ed) add more logging at start
-* [```8a09fb6```](https://github.com/ktmeaton/plague-phylogeography/commit/8a09fb6) sra cache path to launchdir
-* [```d5e67b1```](https://github.com/ktmeaton/plague-phylogeography/commit/d5e67b1) clean up old config
-* [```f913482```](https://github.com/ktmeaton/plague-phylogeography/commit/f913482) limit the assembly ftp opens
-* [```aa5707a```](https://github.com/ktmeaton/plague-phylogeography/commit/aa5707a) better specify resources
-* [```d2d82e1```](https://github.com/ktmeaton/plague-phylogeography/commit/d2d82e1) try to integrate eager back into regular pipeline
-* [```88ad99f```](https://github.com/ktmeaton/plague-phylogeography/commit/88ad99f) remove bam discad unmapped from eager param
-* [```b7741ba```](https://github.com/ktmeaton/plague-phylogeography/commit/b7741ba) add eager profile for github actions
-* [```b7a5a62```](https://github.com/ktmeaton/plague-phylogeography/commit/b7a5a62) add eager profile for github actions
-* [```f09d108```](https://github.com/ktmeaton/plague-phylogeography/commit/f09d108) publish snippy reference folder for debug
-* [```75d7ff7```](https://github.com/ktmeaton/plague-phylogeography/commit/75d7ff7) remove param to discard unmapped
-* [```adc6c0b```](https://github.com/ktmeaton/plague-phylogeography/commit/adc6c0b) adjust pairwise artifact and add ls check
-* [```baa5d25```](https://github.com/ktmeaton/plague-phylogeography/commit/baa5d25) update workflow title
-* [```2d92b1f```](https://github.com/ktmeaton/plague-phylogeography/commit/2d92b1f) upload snippy artifact
-* [```d42360a```](https://github.com/ktmeaton/plague-phylogeography/commit/d42360a) end before snippy multi
-* [```5b191fb```](https://github.com/ktmeaton/plague-phylogeography/commit/5b191fb) convert old pipeline workflow to just sra
-* [```b86adaf```](https://github.com/ktmeaton/plague-phylogeography/commit/b86adaf) create workflow just for testing assembly datasets
-* [```9a63c9b```](https://github.com/ktmeaton/plague-phylogeography/commit/9a63c9b) update treetime docs with jupyter notebook
-* [```b6996a1```](https://github.com/ktmeaton/plague-phylogeography/commit/b6996a1) specify eager ver as var
-* [```d016c38```](https://github.com/ktmeaton/plague-phylogeography/commit/d016c38) update ver to 0.1.4
-* [```5f66752```](https://github.com/ktmeaton/plague-phylogeography/commit/5f66752) allow X char for ambig as well
-* [```5107ae3```](https://github.com/ktmeaton/plague-phylogeography/commit/5107ae3) tidy help docs
-* [```359f6b8```](https://github.com/ktmeaton/plague-phylogeography/commit/359f6b8) add colorbar to rate variation
-* [```9d5c8a7```](https://github.com/ktmeaton/plague-phylogeography/commit/9d5c8a7) successful rate variation tree plot
-* [```94a34ee```](https://github.com/ktmeaton/plague-phylogeography/commit/94a34ee) finish rtt working on tree plotting
-* [```72e69e5```](https://github.com/ktmeaton/plague-phylogeography/commit/72e69e5) ignore notebook file output
-* [```c6e5364```](https://github.com/ktmeaton/plague-phylogeography/commit/c6e5364) separate notebook for full (rtt) analysis)
-* [```28c45e1```](https://github.com/ktmeaton/plague-phylogeography/commit/28c45e1) simply notebooks
-* [```7577cb2```](https://github.com/ktmeaton/plague-phylogeography/commit/7577cb2) new notebook for mugration and node dating
-* [```bfc5e8a```](https://github.com/ktmeaton/plague-phylogeography/commit/bfc5e8a) try vary rate and covary
-* [```266004f```](https://github.com/ktmeaton/plague-phylogeography/commit/266004f) jupyter notebook dependencies
-* [```32a6449```](https://github.com/ktmeaton/plague-phylogeography/commit/32a6449) extend plotting and export for treetime clock
-* [```e22b53e```](https://github.com/ktmeaton/plague-phylogeography/commit/e22b53e) notes about nwk convert
-* [```555e359```](https://github.com/ktmeaton/plague-phylogeography/commit/555e359) add skyline plotting
-* [```cef2bc1```](https://github.com/ktmeaton/plague-phylogeography/commit/cef2bc1) clock testings jupyter notebook
-* [```c35abda```](https://github.com/ktmeaton/plague-phylogeography/commit/c35abda) add timeout config to sra_download
-* [```e04a646```](https://github.com/ktmeaton/plague-phylogeography/commit/e04a646) reduce test cpus to 2
-* [```cdfce45```](https://github.com/ktmeaton/plague-phylogeography/commit/cdfce45) update ori subtree docs
-* [```afc51e9```](https://github.com/ktmeaton/plague-phylogeography/commit/afc51e9) add jupyter notebooks for test plotting
-* [```913de12```](https://github.com/ktmeaton/plague-phylogeography/commit/913de12) update exhibit doc
-* [```23ff447```](https://github.com/ktmeaton/plague-phylogeography/commit/23ff447) fix typo and limit memory
-* [```8b8d7fe```](https://github.com/ktmeaton/plague-phylogeography/commit/8b8d7fe) create the ncbi dir if it doesn't exist
-* [```623c356```](https://github.com/ktmeaton/plague-phylogeography/commit/623c356) fix file checking for sra config
-* [```c040d1b```](https://github.com/ktmeaton/plague-phylogeography/commit/c040d1b) add correct new version with new palette
-* [```5705348```](https://github.com/ktmeaton/plague-phylogeography/commit/5705348) revert copy json
-* [```d5e4d71```](https://github.com/ktmeaton/plague-phylogeography/commit/d5e4d71) update color palette
-* [```0e6fcd6```](https://github.com/ktmeaton/plague-phylogeography/commit/0e6fcd6) more muted blue
-* [```ab5603b```](https://github.com/ktmeaton/plague-phylogeography/commit/ab5603b) add config file for sra_download
-* [```5bfe172```](https://github.com/ktmeaton/plague-phylogeography/commit/5bfe172) fix hex typo
-* [```e038c89```](https://github.com/ktmeaton/plague-phylogeography/commit/e038c89) brighter blue for ORI
-* [```97b73cb```](https://github.com/ktmeaton/plague-phylogeography/commit/97b73cb) color palette change qual
-* [```e4ec1fe```](https://github.com/ktmeaton/plague-phylogeography/commit/e4ec1fe) reinstate Algeria3 biovar
-* [```5421e69```](https://github.com/ktmeaton/plague-phylogeography/commit/5421e69) fix biovar typo
-* [```cdeee94```](https://github.com/ktmeaton/plague-phylogeography/commit/cdeee94) remove biovar info Algeria3
-* [```3f84e72```](https://github.com/ktmeaton/plague-phylogeography/commit/3f84e72) add biovar color map rainbow
-* [```ce2a919```](https://github.com/ktmeaton/plague-phylogeography/commit/ce2a919) update biovars for CIS
-* [```bbbc382```](https://github.com/ktmeaton/plague-phylogeography/commit/bbbc382) troubleshooting error message
-* [```8028b3a```](https://github.com/ktmeaton/plague-phylogeography/commit/8028b3a) mkdir param catch
-* [```74c0fbf```](https://github.com/ktmeaton/plague-phylogeography/commit/74c0fbf) run sra_download before eager test
-* [```db4bd63```](https://github.com/ktmeaton/plague-phylogeography/commit/db4bd63) currently functioning nextstrain section
-* [```9dff87a```](https://github.com/ktmeaton/plague-phylogeography/commit/9dff87a) put geopy explicitly as pip install
-* [```876346b```](https://github.com/ktmeaton/plague-phylogeography/commit/876346b) fix ref and metadata path
-* [```d33f4e7```](https://github.com/ktmeaton/plague-phylogeography/commit/d33f4e7) add nextstrain install
-* [```c4d75d3```](https://github.com/ktmeaton/plague-phylogeography/commit/c4d75d3) remove pestoides biovar fix nepal geo
-* [```89bdd78```](https://github.com/ktmeaton/plague-phylogeography/commit/89bdd78) new clade MED-ANT split
-* [```98a5278```](https://github.com/ktmeaton/plague-phylogeography/commit/98a5278) fix bp error
-* [```059b460```](https://github.com/ktmeaton/plague-phylogeography/commit/059b460) add med antiqua mrca clade
-* [```30e02e0```](https://github.com/ktmeaton/plague-phylogeography/commit/30e02e0) add the caf1 genes
-* [```c057c86```](https://github.com/ktmeaton/plague-phylogeography/commit/c057c86) add modern assembly auspice dataset
-* [```2068e3a```](https://github.com/ktmeaton/plague-phylogeography/commit/2068e3a) test clades pandemic
-* [```3be246d```](https://github.com/ktmeaton/plague-phylogeography/commit/3be246d) fix country geocode errors
-* [```c1e5463```](https://github.com/ktmeaton/plague-phylogeography/commit/c1e5463) rename clades extension
-* [```61d1471```](https://github.com/ktmeaton/plague-phylogeography/commit/61d1471) add the psaC clade
-* [```bd69e23```](https://github.com/ktmeaton/plague-phylogeography/commit/bd69e23) remove excess print statement
-* [```e8f4012```](https://github.com/ktmeaton/plague-phylogeography/commit/e8f4012) tidy install
-* [```0984287```](https://github.com/ktmeaton/plague-phylogeography/commit/0984287) add clades and gene reconstruct
-* [```d097408```](https://github.com/ktmeaton/plague-phylogeography/commit/d097408) add state geo resolution
-* [```f41198a```](https://github.com/ktmeaton/plague-phylogeography/commit/f41198a) fix no data char geocode
-* [```18e9bd3```](https://github.com/ktmeaton/plague-phylogeography/commit/18e9bd3) switch biovar to reconstruct var
-* [```d888500```](https://github.com/ktmeaton/plague-phylogeography/commit/d888500) change time dist measure
-* [```354c4ea```](https://github.com/ktmeaton/plague-phylogeography/commit/354c4ea) delimiter fix
-* [```d2489cf```](https://github.com/ktmeaton/plague-phylogeography/commit/d2489cf) new config for modern assemblies
-* [```2f6e97e```](https://github.com/ktmeaton/plague-phylogeography/commit/2f6e97e) update format Assembly metadata
-* [```a10bd2c```](https://github.com/ktmeaton/plague-phylogeography/commit/a10bd2c) doc update for new geocode
-* [```407d607```](https://github.com/ktmeaton/plague-phylogeography/commit/407d607) doc update for new geocode
-* [```34f4953```](https://github.com/ktmeaton/plague-phylogeography/commit/34f4953) try geopy in nextstrain env
-* [```6d4dfca```](https://github.com/ktmeaton/plague-phylogeography/commit/6d4dfca) update georeferencing
-* [```6d5daef```](https://github.com/ktmeaton/plague-phylogeography/commit/6d5daef) remove test env suffix
-* [```9fb5702```](https://github.com/ktmeaton/plague-phylogeography/commit/9fb5702) update nextstrain env instructions
-* [```b717a4c```](https://github.com/ktmeaton/plague-phylogeography/commit/b717a4c) fix config dir for yaml files
-* [```cfd5631```](https://github.com/ktmeaton/plague-phylogeography/commit/cfd5631) update master table db
-* [```e8f468e```](https://github.com/ktmeaton/plague-phylogeography/commit/e8f468e) complete geo and date
-* [```3afb883```](https://github.com/ktmeaton/plague-phylogeography/commit/3afb883) fixing up georgian geo
-* [```3c6f5a1```](https://github.com/ktmeaton/plague-phylogeography/commit/3c6f5a1) all but missing geo
-* [```742c665```](https://github.com/ktmeaton/plague-phylogeography/commit/742c665) complete Peru geo
-* [```51d470d```](https://github.com/ktmeaton/plague-phylogeography/commit/51d470d) treetime json scripts
-* [```576fc7a```](https://github.com/ktmeaton/plague-phylogeography/commit/576fc7a) test fusing treetime and augur
-* [```a14ad4a```](https://github.com/ktmeaton/plague-phylogeography/commit/a14ad4a) update exhibit for no outgroup
-* [```97e57e1```](https://github.com/ktmeaton/plague-phylogeography/commit/97e57e1) finished India metadata
-* [```2a9600d```](https://github.com/ktmeaton/plague-phylogeography/commit/2a9600d) finish armenia azerbaijan
-* [```2e3afd3```](https://github.com/ktmeaton/plague-phylogeography/commit/2e3afd3) save before eroshenko reconcile
-* [```4b71282```](https://github.com/ktmeaton/plague-phylogeography/commit/4b71282) subdivide geo location into types
-* [```2ef90a9```](https://github.com/ktmeaton/plague-phylogeography/commit/2ef90a9) work on updating anti-plague institute metadata
-* [```1eb2998```](https://github.com/ktmeaton/plague-phylogeography/commit/1eb2998) add plague foci geocoding
-* [```e6cb733```](https://github.com/ktmeaton/plague-phylogeography/commit/e6cb733) fix sed target
-* [```78a2994```](https://github.com/ktmeaton/plague-phylogeography/commit/78a2994) sed in place
-* [```b5b652b```](https://github.com/ktmeaton/plague-phylogeography/commit/b5b652b) update db comments for low cov sample
-* [```f823a84```](https://github.com/ktmeaton/plague-phylogeography/commit/f823a84) change unknown and missing
-* [```70d3f75```](https://github.com/ktmeaton/plague-phylogeography/commit/70d3f75) new metadata format script Assembly
-* [```115fc1c```](https://github.com/ktmeaton/plague-phylogeography/commit/115fc1c) new metadata format script Assembly
-* [```f8b7370```](https://github.com/ktmeaton/plague-phylogeography/commit/f8b7370) add new install commands to pipeline workflow
-* [```4fc9add```](https://github.com/ktmeaton/plague-phylogeography/commit/4fc9add) db update full comments for BioSample
-* [```ad62451```](https://github.com/ktmeaton/plague-phylogeography/commit/ad62451) remove explicit sqlite param in cmd
-* [```f8ae050```](https://github.com/ktmeaton/plague-phylogeography/commit/f8ae050) add eager rev to help cmd
-* [```968efa5```](https://github.com/ktmeaton/plague-phylogeography/commit/968efa5) more comprehensive install test
-* [```32a1978```](https://github.com/ktmeaton/plague-phylogeography/commit/32a1978) test graphviz and eager separately
-* [```2da21fb```](https://github.com/ktmeaton/plague-phylogeography/commit/2da21fb) fix optimize typo
-* [```ce41a0d```](https://github.com/ktmeaton/plague-phylogeography/commit/ce41a0d) add SCDS2020 to showcase
-* [```5563327```](https://github.com/ktmeaton/plague-phylogeography/commit/5563327) add showcase section
-* [```6dfd821```](https://github.com/ktmeaton/plague-phylogeography/commit/6dfd821) try to fix rename loop
-* [```029fb8c```](https://github.com/ktmeaton/plague-phylogeography/commit/029fb8c) attempt to fix snippy dedup bam RG issue
-* [```25beda6```](https://github.com/ktmeaton/plague-phylogeography/commit/25beda6) correct max sra from 1 to 2
-* [```08772a1```](https://github.com/ktmeaton/plague-phylogeography/commit/08772a1) simplify pipeline
-* [```b9347ed```](https://github.com/ktmeaton/plague-phylogeography/commit/b9347ed) add config param iqtree_runs
-* [```c46c2c5```](https://github.com/ktmeaton/plague-phylogeography/commit/c46c2c5) fix branch support param
-* [```3cebf05```](https://github.com/ktmeaton/plague-phylogeography/commit/3cebf05) reduce testing assembly, disable branch support default
-* [```c3e5426```](https://github.com/ktmeaton/plague-phylogeography/commit/c3e5426) reducing testing and example to 1 iqtree run
-* [```2f7fbb3```](https://github.com/ktmeaton/plague-phylogeography/commit/2f7fbb3) rename phylo-env env
-* [```48ef9fc```](https://github.com/ktmeaton/plague-phylogeography/commit/48ef9fc) update environment name and tidy env
-* [```1f25f5b```](https://github.com/ktmeaton/plague-phylogeography/commit/1f25f5b) try launchdir not basedir for output
-* [```4f6ef19```](https://github.com/ktmeaton/plague-phylogeography/commit/4f6ef19) update output with time
-* [```366457f```](https://github.com/ktmeaton/plague-phylogeography/commit/366457f) use absolute link to logo
-* [```9f45476```](https://github.com/ktmeaton/plague-phylogeography/commit/9f45476) add logo
-* [```6b6b0ee```](https://github.com/ktmeaton/plague-phylogeography/commit/6b6b0ee) remove extra echo true
-* [```43d115a```](https://github.com/ktmeaton/plague-phylogeography/commit/43d115a) add license
-* [```7e7f2d1```](https://github.com/ktmeaton/plague-phylogeography/commit/7e7f2d1) update move and workflow
-* [```84a0338```](https://github.com/ktmeaton/plague-phylogeography/commit/84a0338) move config files to config dir
-* [```1e2c852```](https://github.com/ktmeaton/plague-phylogeography/commit/1e2c852) remove old annot files
-* [```1d7d336```](https://github.com/ktmeaton/plague-phylogeography/commit/1d7d336) correct iqtree param
-* [```637019d```](https://github.com/ktmeaton/plague-phylogeography/commit/637019d) update for default database
-* [```495ed41```](https://github.com/ktmeaton/plague-phylogeography/commit/495ed41) add more iqtree param
-* [```af33e64```](https://github.com/ktmeaton/plague-phylogeography/commit/af33e64) add more iqtree param
-* [```7caf690```](https://github.com/ktmeaton/plague-phylogeography/commit/7caf690) make sqlite parameter a default
-* [```52e8d5e```](https://github.com/ktmeaton/plague-phylogeography/commit/52e8d5e) set a default sqlite database to yp
-* [```cfa265e```](https://github.com/ktmeaton/plague-phylogeography/commit/cfa265e) add optional outgroup to iqtree
-* [```77ddfd3```](https://github.com/ktmeaton/plague-phylogeography/commit/77ddfd3) list conda env
-* [```021b911```](https://github.com/ktmeaton/plague-phylogeography/commit/021b911) mock of outgroup process for iqtree
-* [```369c52c```](https://github.com/ktmeaton/plague-phylogeography/commit/369c52c) fix environment name bug to phylo-dev
-* [```c5b35a1```](https://github.com/ktmeaton/plague-phylogeography/commit/c5b35a1) add conda activate statements
-* [```16371c2```](https://github.com/ktmeaton/plague-phylogeography/commit/16371c2) add process outgroup_download
-* [```31788be```](https://github.com/ktmeaton/plague-phylogeography/commit/31788be) make dynamic rng
-* [```19f6b6d```](https://github.com/ktmeaton/plague-phylogeography/commit/19f6b6d) add example output
-* [```240b76f```](https://github.com/ktmeaton/plague-phylogeography/commit/240b76f) update trigers with new main and environment
-* [```accb443```](https://github.com/ktmeaton/plague-phylogeography/commit/accb443) function snippy pairwise for fna
-* [```873ddbf```](https://github.com/ktmeaton/plague-phylogeography/commit/873ddbf) functional fna bam flatten collect
-* [```e2299c6```](https://github.com/ktmeaton/plague-phylogeography/commit/e2299c6) BROKEN adding bam to snippy pairwise
-* [```6e33611```](https://github.com/ktmeaton/plague-phylogeography/commit/6e33611) fix the terrible if statements back to when
-* [```4a2343c```](https://github.com/ktmeaton/plague-phylogeography/commit/4a2343c) put into all one job
-* [```54327a7```](https://github.com/ktmeaton/plague-phylogeography/commit/54327a7) fix sra typo spacing
-* [```c036203```](https://github.com/ktmeaton/plague-phylogeography/commit/c036203) fix typo and pipeline call
-* [```eef44c4```](https://github.com/ktmeaton/plague-phylogeography/commit/eef44c4) fix typo and pipeline call
-* [```06f7313```](https://github.com/ktmeaton/plague-phylogeography/commit/06f7313) condense pipeline to one workflow
-* [```02a082c```](https://github.com/ktmeaton/plague-phylogeography/commit/02a082c) put nf eager after plague phylo
-* [```d71767e```](https://github.com/ktmeaton/plague-phylogeography/commit/d71767e) condense and rename phylo-env to environment.yaml
-* [```9171823```](https://github.com/ktmeaton/plague-phylogeography/commit/9171823) pull nf eager in two steps
-* [```4195f44```](https://github.com/ktmeaton/plague-phylogeography/commit/4195f44) remove nf eager rev code
-* [```eb67aa5```](https://github.com/ktmeaton/plague-phylogeography/commit/eb67aa5) hard code rev nf eager
-* [```8953012```](https://github.com/ktmeaton/plague-phylogeography/commit/8953012) try to fix nf eager install
-* [```68e6498```](https://github.com/ktmeaton/plague-phylogeography/commit/68e6498) fix workflow typo
-* [```5fdb9d9```](https://github.com/ktmeaton/plague-phylogeography/commit/5fdb9d9) change install to nextflow pull
-* [```c345590```](https://github.com/ktmeaton/plague-phylogeography/commit/c345590) remove multiqc_config manual handling
-* [```7261e43```](https://github.com/ktmeaton/plague-phylogeography/commit/7261e43) remove eager multiqc_config manual
-* [```030e777```](https://github.com/ktmeaton/plague-phylogeography/commit/030e777) rename pipeline.nf to main.nf
-* [```e281284```](https://github.com/ktmeaton/plague-phylogeography/commit/e281284) fixed resume option for eager process
-* [```ee3b344```](https://github.com/ktmeaton/plague-phylogeography/commit/ee3b344) control eager rev as var
-* [```42fa26a```](https://github.com/ktmeaton/plague-phylogeography/commit/42fa26a) add graphviz to env
-* [```fa20b29```](https://github.com/ktmeaton/plague-phylogeography/commit/fa20b29) locally functioning eager with new work dir
-* [```bd6bd73```](https://github.com/ktmeaton/plague-phylogeography/commit/bd6bd73) new install instructions
-* [```a343b34```](https://github.com/ktmeaton/plague-phylogeography/commit/a343b34) add example output
-* [```672a561```](https://github.com/ktmeaton/plague-phylogeography/commit/672a561) move multiqic files to config dir
-* [```108a90a```](https://github.com/ktmeaton/plague-phylogeography/commit/108a90a) run eager test outside pipeline
-* [```331bf04```](https://github.com/ktmeaton/plague-phylogeography/commit/331bf04) remove eager for testing
-* [```14c076e```](https://github.com/ktmeaton/plague-phylogeography/commit/14c076e) test perl5lib setup
-* [```0826b53```](https://github.com/ktmeaton/plague-phylogeography/commit/0826b53) now testing assembly and sra together
-* [```3bcb124```](https://github.com/ktmeaton/plague-phylogeography/commit/3bcb124) echo PERL5LIB debug
-* [```1cf09d3```](https://github.com/ktmeaton/plague-phylogeography/commit/1cf09d3) remove old notes file
-* [```0257b2d```](https://github.com/ktmeaton/plague-phylogeography/commit/0257b2d) remove old nextstrain dir
-* [```076fa7e```](https://github.com/ktmeaton/plague-phylogeography/commit/076fa7e) remove eager dir
-* [```847d8d0```](https://github.com/ktmeaton/plague-phylogeography/commit/847d8d0) m2r update readme and upload html artifact
-* [```1ca39ff```](https://github.com/ktmeaton/plague-phylogeography/commit/1ca39ff) update README docs
-* [```207f650```](https://github.com/ktmeaton/plague-phylogeography/commit/207f650) edit modern assembly section
-* [```cd4d870```](https://github.com/ktmeaton/plague-phylogeography/commit/cd4d870) improve install and quick start
-* [```7f8392f```](https://github.com/ktmeaton/plague-phylogeography/commit/7f8392f) try installing nextflow into eager conda env
-* [```299b0fb```](https://github.com/ktmeaton/plague-phylogeography/commit/299b0fb) rearrange to optimze eager install
-* [```656a19d```](https://github.com/ktmeaton/plague-phylogeography/commit/656a19d) fix workflow errors
-* [```51cd334```](https://github.com/ktmeaton/plague-phylogeography/commit/51cd334) rearrange install nextflow first
-* [```cd46a59```](https://github.com/ktmeaton/plague-phylogeography/commit/cd46a59) attempt conda create with eager env
-* [```4f31199```](https://github.com/ktmeaton/plague-phylogeography/commit/4f31199) update eager env to dev 2.2.0
-* [```6bef53a```](https://github.com/ktmeaton/plague-phylogeography/commit/6bef53a) fix broken sra workflow rule
-* [```50d795e```](https://github.com/ktmeaton/plague-phylogeography/commit/50d795e) greatly simplify SRA pipeline instructions
-* [```54ae4dd```](https://github.com/ktmeaton/plague-phylogeography/commit/54ae4dd) have eager create conda env
-* [```b4936c6```](https://github.com/ktmeaton/plague-phylogeography/commit/b4936c6) add eager-env from dev
-* [```ba09041```](https://github.com/ktmeaton/plague-phylogeography/commit/ba09041) add eager to test workflow
-* [```c8dea94```](https://github.com/ktmeaton/plague-phylogeography/commit/c8dea94) move paper to new repository
-* [```673035d```](https://github.com/ktmeaton/plague-phylogeography/commit/673035d) new sra testing workflow
-* [```8f7c6d2```](https://github.com/ktmeaton/plague-phylogeography/commit/8f7c6d2) functioning sra download
-* [```7530570```](https://github.com/ktmeaton/plague-phylogeography/commit/7530570) large update and script bugfix
-* [```055124f```](https://github.com/ktmeaton/plague-phylogeography/commit/055124f) add D101 query to ncbimeta BioSample search
-* [```8a291d3```](https://github.com/ktmeaton/plague-phylogeography/commit/8a291d3) finished commenting Ancient projects round 1
-* [```bc5f7f4```](https://github.com/ktmeaton/plague-phylogeography/commit/bc5f7f4) update EAGER ancient comments and bioproject acc
-* [```072ecbf```](https://github.com/ktmeaton/plague-phylogeography/commit/072ecbf) add notes for all EAGER run
-* [```40c403d```](https://github.com/ktmeaton/plague-phylogeography/commit/40c403d) update the EAGER and KEEP comments
-* [```4fa3344```](https://github.com/ktmeaton/plague-phylogeography/commit/4fa3344) update directories
-* [```c38a60c```](https://github.com/ktmeaton/plague-phylogeography/commit/c38a60c) update directories
-* [```8c9d5c7```](https://github.com/ktmeaton/plague-phylogeography/commit/8c9d5c7) successful eager run test
-* [```297bc83```](https://github.com/ktmeaton/plague-phylogeography/commit/297bc83) add black and flake8
-* [```be90621```](https://github.com/ktmeaton/plague-phylogeography/commit/be90621) instructions for sra download
-* [```39c60bc```](https://github.com/ktmeaton/plague-phylogeography/commit/39c60bc) change sra download dir
-* [```a3adedc```](https://github.com/ktmeaton/plague-phylogeography/commit/a3adedc) change sra download dir
-* [```0a2b960```](https://github.com/ktmeaton/plague-phylogeography/commit/0a2b960) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```20ee84a```](https://github.com/ktmeaton/plague-phylogeography/commit/20ee84a) update eager tsv script
-* [```d48b56b```](https://github.com/ktmeaton/plague-phylogeography/commit/d48b56b) sra notes 8291
-* [```6203356```](https://github.com/ktmeaton/plague-phylogeography/commit/6203356) add outgroups ftp links
-* [```8cd7905```](https://github.com/ktmeaton/plague-phylogeography/commit/8cd7905) note add outgroup
-* [```1a2099e```](https://github.com/ktmeaton/plague-phylogeography/commit/1a2099e) Set theme jekyll-theme-cayman
-* [```92b2f52```](https://github.com/ktmeaton/plague-phylogeography/commit/92b2f52) Set theme jekyll-theme-dinky
-* [```ed413e3```](https://github.com/ktmeaton/plague-phylogeography/commit/ed413e3) add good debate lit sources
-* [```4eca9c2```](https://github.com/ktmeaton/plague-phylogeography/commit/4eca9c2) reorganize paper text
-* [```b9f9c1f```](https://github.com/ktmeaton/plague-phylogeography/commit/b9f9c1f) note about breaking up snippy
-* [```6e534e0```](https://github.com/ktmeaton/plague-phylogeography/commit/6e534e0) get artifacts from test outdir
-* [```64e22d6```](https://github.com/ktmeaton/plague-phylogeography/commit/64e22d6) remove eager from pipeline for now
-* [```591f1fb```](https://github.com/ktmeaton/plague-phylogeography/commit/591f1fb) add sql command select
-* [```940a235```](https://github.com/ktmeaton/plague-phylogeography/commit/940a235) reset ncbimeta pip conflicts pyyaml
-* [```01a52c4```](https://github.com/ktmeaton/plague-phylogeography/commit/01a52c4) allow img inline html
-* [```46f4753```](https://github.com/ktmeaton/plague-phylogeography/commit/46f4753) run pipeline if env yaml updates
-* [```70889ac```](https://github.com/ktmeaton/plague-phylogeography/commit/70889ac) switch ncbimeta to pip install
-* [```8029450```](https://github.com/ktmeaton/plague-phylogeography/commit/8029450) specify commit rev for eager pull
-* [```b0e7b91```](https://github.com/ktmeaton/plague-phylogeography/commit/b0e7b91) add assignee to other issues
-* [```c0a2238```](https://github.com/ktmeaton/plague-phylogeography/commit/c0a2238) lint CHANGELOG
-* [```407a244```](https://github.com/ktmeaton/plague-phylogeography/commit/407a244) add PR and issue templates
-* [```cb0d268```](https://github.com/ktmeaton/plague-phylogeography/commit/cb0d268) add pipeline steps move usage to rtd
-* [```d0d5d67```](https://github.com/ktmeaton/plague-phylogeography/commit/d0d5d67) add assembly pipeline
-* [```b9dd5f1```](https://github.com/ktmeaton/plague-phylogeography/commit/b9dd5f1) up to verify samples
-* [```06a9c22```](https://github.com/ktmeaton/plague-phylogeography/commit/06a9c22) fix headings level
-* [```98fe92d```](https://github.com/ktmeaton/plague-phylogeography/commit/98fe92d) overhaul section headers
-* [```083f109```](https://github.com/ktmeaton/plague-phylogeography/commit/083f109) document database curation
-* [```a4a56d7```](https://github.com/ktmeaton/plague-phylogeography/commit/a4a56d7) test sublist
-* [```245463d```](https://github.com/ktmeaton/plague-phylogeography/commit/245463d) remove treetime issue notes
-* [```2dcac55```](https://github.com/ktmeaton/plague-phylogeography/commit/2dcac55) remove old markdown config
-* [```66e2024```](https://github.com/ktmeaton/plague-phylogeography/commit/66e2024) remove old trace files
-* [```44896ad```](https://github.com/ktmeaton/plague-phylogeography/commit/44896ad) cleanup morelli and cui
-* [```60db533```](https://github.com/ktmeaton/plague-phylogeography/commit/60db533) test main render
-* [```b9ec0ae```](https://github.com/ktmeaton/plague-phylogeography/commit/b9ec0ae) update ncbimeta to v0.6.6
-* [```2921935```](https://github.com/ktmeaton/plague-phylogeography/commit/2921935) lint exhibit_link
-* [```b7362ce```](https://github.com/ktmeaton/plague-phylogeography/commit/b7362ce) lint README
-* [```cd31ea7```](https://github.com/ktmeaton/plague-phylogeography/commit/cd31ea7) lint main rst
-* [```4494e12```](https://github.com/ktmeaton/plague-phylogeography/commit/4494e12) lint README
-* [```63e2fc1```](https://github.com/ktmeaton/plague-phylogeography/commit/63e2fc1) lint README
-* [```f69ac02```](https://github.com/ktmeaton/plague-phylogeography/commit/f69ac02) lint README
+* [```b0d6107b```](https://github.com/ktmeaton/plague-phylogeography/commit/b0d6107b) change DB var in exhibit docs
+* [```cf23b488```](https://github.com/ktmeaton/plague-phylogeography/commit/cf23b488) update docs
+* [```7b04fc15```](https://github.com/ktmeaton/plague-phylogeography/commit/7b04fc15) add a CodeSpaces link to test
+* [```6fa9e24d```](https://github.com/ktmeaton/plague-phylogeography/commit/6fa9e24d) Update contributing and templates, pull docs"
+* [```5d16e3fb```](https://github.com/ktmeaton/plague-phylogeography/commit/5d16e3fb) update contributing and templates
+* [```5037c7d4```](https://github.com/ktmeaton/plague-phylogeography/commit/5037c7d4) update modern and ancient commands
+* [```2faa8e72```](https://github.com/ktmeaton/plague-phylogeography/commit/2faa8e72) update docs
+* [```c69570ff```](https://github.com/ktmeaton/plague-phylogeography/commit/c69570ff) Add execute to github, pull docs
+* [```af81b480```](https://github.com/ktmeaton/plague-phylogeography/commit/af81b480) add execute to github
+* [```b752a97d```](https://github.com/ktmeaton/plague-phylogeography/commit/b752a97d) add execute to github
+* [```2bafa866```](https://github.com/ktmeaton/plague-phylogeography/commit/2bafa866) update docs
+* [```81a4e4e7```](https://github.com/ktmeaton/plague-phylogeography/commit/81a4e4e7) generic loci extract, pull docs
+* [```e558a03f```](https://github.com/ktmeaton/plague-phylogeography/commit/e558a03f) remove param sqlite
+* [```38370613```](https://github.com/ktmeaton/plague-phylogeography/commit/38370613) tackled some high and low priorities
+* [```d4c8bfa3```](https://github.com/ktmeaton/plague-phylogeography/commit/d4c8bfa3) update ncbimeta params
+* [```44d0b950```](https://github.com/ktmeaton/plague-phylogeography/commit/44d0b950) allow generic locus extraction
+* [```19880268```](https://github.com/ktmeaton/plague-phylogeography/commit/19880268) change from split to generic extract
+* [```1caa43c7```](https://github.com/ktmeaton/plague-phylogeography/commit/1caa43c7) change ref genome add locus info
+* [```3305261d```](https://github.com/ktmeaton/plague-phylogeography/commit/3305261d) update docs
+* [```fc47ea98```](https://github.com/ktmeaton/plague-phylogeography/commit/fc47ea98) Change local to custom, pull docs
+* [```64ebbab8```](https://github.com/ktmeaton/plague-phylogeography/commit/64ebbab8) change custom to local
+* [```563671ef```](https://github.com/ktmeaton/plague-phylogeography/commit/563671ef) update docs
+* [```22b0577a```](https://github.com/ktmeaton/plague-phylogeography/commit/22b0577a) fix pipeline var typo
+* [```02a9237a```](https://github.com/ktmeaton/plague-phylogeography/commit/02a9237a) fix goofy sql escape char
+* [```e3cf4cb3```](https://github.com/ktmeaton/plague-phylogeography/commit/e3cf4cb3) change custom dir to example
+* [```1c4bb3d5```](https://github.com/ktmeaton/plague-phylogeography/commit/1c4bb3d5) test relative paths and merge docs
+* [```582a4ed1```](https://github.com/ktmeaton/plague-phylogeography/commit/582a4ed1) try workflows with relative paths
+* [```3e4189c4```](https://github.com/ktmeaton/plague-phylogeography/commit/3e4189c4) update docs
+* [```7c1e065a```](https://github.com/ktmeaton/plague-phylogeography/commit/7c1e065a) proper channel support for ncbimeta_annot
+* [```87440bb2```](https://github.com/ktmeaton/plague-phylogeography/commit/87440bb2) fix indentation
+* [```fd26b5ac```](https://github.com/ktmeaton/plague-phylogeography/commit/fd26b5ac) update workflow job name
+* [```a9156a05```](https://github.com/ktmeaton/plague-phylogeography/commit/a9156a05) add biosample backup tsv
+* [```1e105223```](https://github.com/ktmeaton/plague-phylogeography/commit/1e105223) add echo true to ncbimeta processes and eager
+* [```a6b96059```](https://github.com/ktmeaton/plague-phylogeography/commit/a6b96059) add proper slash and test db path
+* [```448100f7```](https://github.com/ktmeaton/plague-phylogeography/commit/448100f7) add proper slash and test db path
+* [```0643b183```](https://github.com/ktmeaton/plague-phylogeography/commit/0643b183) check pwd
+* [```80829dc5```](https://github.com/ktmeaton/plague-phylogeography/commit/80829dc5) remove bad Biosample_id column
+* [```e0fa2229```](https://github.com/ktmeaton/plague-phylogeography/commit/e0fa2229) get path for test db
+* [```61938fe1```](https://github.com/ktmeaton/plague-phylogeography/commit/61938fe1) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```13b13e66```](https://github.com/ktmeaton/plague-phylogeography/commit/13b13e66) extend runtime and use resume
+* [```d9a1a6fb```](https://github.com/ktmeaton/plague-phylogeography/commit/d9a1a6fb) update docs
+* [```2e198788```](https://github.com/ktmeaton/plague-phylogeography/commit/2e198788) attempt to put api param in quotes
+* [```a82ca7c1```](https://github.com/ktmeaton/plague-phylogeography/commit/a82ca7c1) remove sed replacment from config file
+* [```a16ef0a3```](https://github.com/ktmeaton/plague-phylogeography/commit/a16ef0a3) enforce black ver
+* [```8646c0b1```](https://github.com/ktmeaton/plague-phylogeography/commit/8646c0b1) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```c87e885c```](https://github.com/ktmeaton/plague-phylogeography/commit/c87e885c) test pipeline db after ncbimeta 0.7.0 release
+* [```dc6b8593```](https://github.com/ktmeaton/plague-phylogeography/commit/dc6b8593) update docs
+* [```07b553c1```](https://github.com/ktmeaton/plague-phylogeography/commit/07b553c1) test workflows for ncbimeta v0.7.0
+* [```5ca2480e```](https://github.com/ktmeaton/plague-phylogeography/commit/5ca2480e) try workflow after restricting biopython
+* [```30a047d9```](https://github.com/ktmeaton/plague-phylogeography/commit/30a047d9) restrict biopython to 1.74
+* [```7219e2d4```](https://github.com/ktmeaton/plague-phylogeography/commit/7219e2d4) make note of biopython restriction
+* [```642d6a54```](https://github.com/ktmeaton/plague-phylogeography/commit/642d6a54) try to customize db yaml
+* [```1005284d```](https://github.com/ktmeaton/plague-phylogeography/commit/1005284d) recome sqlite param from db create
+* [```b55f2fa6```](https://github.com/ktmeaton/plague-phylogeography/commit/b55f2fa6) note to troubleshoot ncbimeta error
+* [```e141021b```](https://github.com/ktmeaton/plague-phylogeography/commit/e141021b) add python 3.7 to conda env
+* [```4e422bef```](https://github.com/ktmeaton/plague-phylogeography/commit/4e422bef) use relative path for custom reads
+* [```99bf05c0```](https://github.com/ktmeaton/plague-phylogeography/commit/99bf05c0) remove nextstrain uninstall
+* [```930e2bc9```](https://github.com/ktmeaton/plague-phylogeography/commit/930e2bc9) remove nextrain env cache
+* [```ee905fb9```](https://github.com/ktmeaton/plague-phylogeography/commit/ee905fb9) try using the var HOME for custom tsv
+* [```7b5c9ffb```](https://github.com/ktmeaton/plague-phylogeography/commit/7b5c9ffb) fix double tsv file input for eager
+* [```723d32e7```](https://github.com/ktmeaton/plague-phylogeography/commit/723d32e7) add linting notes and process docs
+* [```21be21c2```](https://github.com/ktmeaton/plague-phylogeography/commit/21be21c2) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```a7e2c459```](https://github.com/ktmeaton/plague-phylogeography/commit/a7e2c459) test doc workflow when no file changes
+* [```6ce2b205```](https://github.com/ktmeaton/plague-phylogeography/commit/6ce2b205) update docs
+* [```e46d58e7```](https://github.com/ktmeaton/plague-phylogeography/commit/e46d58e7) try separating push
+* [```157b2c7e```](https://github.com/ktmeaton/plague-phylogeography/commit/157b2c7e) try or statements for commit and push
+* [```7e452ad4```](https://github.com/ktmeaton/plague-phylogeography/commit/7e452ad4) add debugging statement
+* [```94a0a038```](https://github.com/ktmeaton/plague-phylogeography/commit/94a0a038) try deleting untrack files again
+* [```fcfed034```](https://github.com/ktmeaton/plague-phylogeography/commit/fcfed034) try deleting untrack files again
+* [```9c054878```](https://github.com/ktmeaton/plague-phylogeography/commit/9c054878) update docs process_all
+* [```ab8aaba3```](https://github.com/ktmeaton/plague-phylogeography/commit/ab8aaba3) escape wildcard characters
+* [```027d0985```](https://github.com/ktmeaton/plague-phylogeography/commit/027d0985) test upload process_all
+* [```97e262b7```](https://github.com/ktmeaton/plague-phylogeography/commit/97e262b7) remove old process docs
+* [```14763acd```](https://github.com/ktmeaton/plague-phylogeography/commit/14763acd) test untracking auto docs
+* [```0d7763d7```](https://github.com/ktmeaton/plague-phylogeography/commit/0d7763d7) update docs process_all
+* [```484b7493```](https://github.com/ktmeaton/plague-phylogeography/commit/484b7493) use section text in main and process_docs
+* [```dccdfb90```](https://github.com/ktmeaton/plague-phylogeography/commit/dccdfb90) commit updated process_all if changed
+* [```ad119dbc```](https://github.com/ktmeaton/plague-phylogeography/commit/ad119dbc) docs workflow depends on process_docs script
+* [```a68cab73```](https://github.com/ktmeaton/plague-phylogeography/commit/a68cab73) run python linter
+* [```c9ff1828```](https://github.com/ktmeaton/plague-phylogeography/commit/c9ff1828) test linter
+* [```2403546e```](https://github.com/ktmeaton/plague-phylogeography/commit/2403546e) test linter
+* [```7ddcfde9```](https://github.com/ktmeaton/plague-phylogeography/commit/7ddcfde9) workflow creates process_all from docstrings
+* [```eaefcdf0```](https://github.com/ktmeaton/plague-phylogeography/commit/eaefcdf0) auto docstring build
+* [```aff27f44```](https://github.com/ktmeaton/plague-phylogeography/commit/aff27f44) add process docs script
+* [```079a1157```](https://github.com/ktmeaton/plague-phylogeography/commit/079a1157) restore no channel specify, remove excess docs
+* [```26da567c```](https://github.com/ktmeaton/plague-phylogeography/commit/26da567c) re-add conda forge channel
+* [```08928d56```](https://github.com/ktmeaton/plague-phylogeography/commit/08928d56) don't install nextstrain env
+* [```b20299b3```](https://github.com/ktmeaton/plague-phylogeography/commit/b20299b3) don't install nextstrain env
+* [```cd5b0a9c```](https://github.com/ktmeaton/plague-phylogeography/commit/cd5b0a9c) don't install nextstrain env
+* [```137b258a```](https://github.com/ktmeaton/plague-phylogeography/commit/137b258a) try removing conda-forge from phylo env
+* [```7ae5af51```](https://github.com/ktmeaton/plague-phylogeography/commit/7ae5af51) change local tsv to nf paths
+* [```7dc48220```](https://github.com/ktmeaton/plague-phylogeography/commit/7dc48220) change local tsv to nf paths
+* [```b32736cc```](https://github.com/ktmeaton/plague-phylogeography/commit/b32736cc) fix sqlite db repo var
+* [```9e41768d```](https://github.com/ktmeaton/plague-phylogeography/commit/9e41768d) change github repo and sha var
+* [```2d377d58```](https://github.com/ktmeaton/plague-phylogeography/commit/2d377d58) test the db pipeline
+* [```ab3d7baa```](https://github.com/ktmeaton/plague-phylogeography/commit/ab3d7baa) Merge in new README
+* [```6fa92dae```](https://github.com/ktmeaton/plague-phylogeography/commit/6fa92dae) retry github repo var
+* [```4ba5ba12```](https://github.com/ktmeaton/plague-phylogeography/commit/4ba5ba12) update docs README
+* [```33e47b5f```](https://github.com/ktmeaton/plague-phylogeography/commit/33e47b5f) link point to nf path rather than local
+* [```723558ec```](https://github.com/ktmeaton/plague-phylogeography/commit/723558ec) now testing ncbimeta update v0.6.6
+* [```fd3b6a30```](https://github.com/ktmeaton/plague-phylogeography/commit/fd3b6a30) update install script to use repo and sha
+* [```a006df25```](https://github.com/ktmeaton/plague-phylogeography/commit/a006df25) fix conda update input
+* [```433088c5```](https://github.com/ktmeaton/plague-phylogeography/commit/433088c5) test ncbimeta 0.6.6 and auto update conda
+* [```f53e0dc1```](https://github.com/ktmeaton/plague-phylogeography/commit/f53e0dc1) remove debug and test load cache
+* [```95b60284```](https://github.com/ktmeaton/plague-phylogeography/commit/95b60284) backup manual annotations
+* [```c64caf31```](https://github.com/ktmeaton/plague-phylogeography/commit/c64caf31) search for conda.sh in home or usr share
+* [```efe9a655```](https://github.com/ktmeaton/plague-phylogeography/commit/efe9a655) search for conda.sh in home or usr share
+* [```9b8f8cb0```](https://github.com/ktmeaton/plague-phylogeography/commit/9b8f8cb0) test conda exe location
+* [```85750db7```](https://github.com/ktmeaton/plague-phylogeography/commit/85750db7) inspect profile.d dir
+* [```6480e39c```](https://github.com/ktmeaton/plague-phylogeography/commit/6480e39c) more debug to check usr share path
+* [```5754fb3c```](https://github.com/ktmeaton/plague-phylogeography/commit/5754fb3c) extra debug statements to check cache
+* [```7fa5de19```](https://github.com/ktmeaton/plague-phylogeography/commit/7fa5de19) retry install with longer runtime
+* [```ce23bf6d```](https://github.com/ktmeaton/plague-phylogeography/commit/ce23bf6d) specify repo and sha with install script
+* [```fa318c51```](https://github.com/ktmeaton/plague-phylogeography/commit/fa318c51) update with env name
+* [```88995fe9```](https://github.com/ktmeaton/plague-phylogeography/commit/88995fe9) fix header lint spacing
+* [```72a5bcda```](https://github.com/ktmeaton/plague-phylogeography/commit/72a5bcda) update 0.1.4 changes and to do
+* [```50676156```](https://github.com/ktmeaton/plague-phylogeography/commit/50676156) ignore sra dir
+* [```62e00c9d```](https://github.com/ktmeaton/plague-phylogeography/commit/62e00c9d) try local data pipeline
+* [```a8b15140```](https://github.com/ktmeaton/plague-phylogeography/commit/a8b15140) more flexible tsv naming
+* [```414c07bb```](https://github.com/ktmeaton/plague-phylogeography/commit/414c07bb) attempt more local reads to avoid 0 SNP call
+* [```730161a7```](https://github.com/ktmeaton/plague-phylogeography/commit/730161a7) more flexible custom tsv naming
+* [```23d6ba32```](https://github.com/ktmeaton/plague-phylogeography/commit/23d6ba32) allow local reads and assemblies
+* [```e34842e5```](https://github.com/ktmeaton/plague-phylogeography/commit/e34842e5) add java install notes
+* [```f8974787```](https://github.com/ktmeaton/plague-phylogeography/commit/f8974787) add new to do
+* [```5788318f```](https://github.com/ktmeaton/plague-phylogeography/commit/5788318f) comment to explain check max vals
+* [```e5c3344b```](https://github.com/ktmeaton/plague-phylogeography/commit/e5c3344b) remove combine pipeline
+* [```eb6aacef```](https://github.com/ktmeaton/plague-phylogeography/commit/eb6aacef) reset check max time
+* [```264df9ff```](https://github.com/ktmeaton/plague-phylogeography/commit/264df9ff) begin commenting low coverage EAGER Ancient
+* [```37281bc3```](https://github.com/ktmeaton/plague-phylogeography/commit/37281bc3) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```52454a3f```](https://github.com/ktmeaton/plague-phylogeography/commit/52454a3f) add mv statement
+* [```1dfd7cf0```](https://github.com/ktmeaton/plague-phylogeography/commit/1dfd7cf0) update docs README
+* [```5542e3c7```](https://github.com/ktmeaton/plague-phylogeography/commit/5542e3c7) move eager output of multiqc and pipeline_info
+* [```f8f53875```](https://github.com/ktmeaton/plague-phylogeography/commit/f8f53875) add conda links
+* [```eceaebed```](https://github.com/ktmeaton/plague-phylogeography/commit/eceaebed) sanity commit
+* [```ee4a33e8```](https://github.com/ktmeaton/plague-phylogeography/commit/ee4a33e8) lower timeouts back down ot 30 min
+* [```f94d8233```](https://github.com/ktmeaton/plague-phylogeography/commit/f94d8233) limit iqtree threads, remove bnni param
+* [```275563f1```](https://github.com/ktmeaton/plague-phylogeography/commit/275563f1) try extending runtime limit
+* [```dddb53e1```](https://github.com/ktmeaton/plague-phylogeography/commit/dddb53e1) add proper gh resources
+* [```166532fb```](https://github.com/ktmeaton/plague-phylogeography/commit/166532fb) fix bam readgroup error snippy
+* [```6cd5a8ee```](https://github.com/ktmeaton/plague-phylogeography/commit/6cd5a8ee) change output of eager to the lib merged bam
+* [```c50013c4```](https://github.com/ktmeaton/plague-phylogeography/commit/c50013c4) rearrange sra config settings
+* [```fcb34816```](https://github.com/ktmeaton/plague-phylogeography/commit/fcb34816) try new workflow with combine
+* [```e27d08d4```](https://github.com/ktmeaton/plague-phylogeography/commit/e27d08d4) add trace info to docs
+* [```2b0543f5```](https://github.com/ktmeaton/plague-phylogeography/commit/2b0543f5) if sra cache is already set, retrieve it
+* [```ab96ecb5```](https://github.com/ktmeaton/plague-phylogeography/commit/ab96ecb5) add dev to ver number
+* [```66671d65```](https://github.com/ktmeaton/plague-phylogeography/commit/66671d65) keep outdir consistent so caching works
+* [```8f440ac5```](https://github.com/ktmeaton/plague-phylogeography/commit/8f440ac5) update modern and ancient docs
+* [```5982d097```](https://github.com/ktmeaton/plague-phylogeography/commit/5982d097) Testing sra validate and metadata linking
+* [```863d0df2```](https://github.com/ktmeaton/plague-phylogeography/commit/863d0df2) validate sra download, add biosample acc to path
+* [```7248e291```](https://github.com/ktmeaton/plague-phylogeography/commit/7248e291) add biosample acc to fastq path
+* [```a1f05152```](https://github.com/ktmeaton/plague-phylogeography/commit/a1f05152) update docs README
+* [```1099d026```](https://github.com/ktmeaton/plague-phylogeography/commit/1099d026) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```2db7ec53```](https://github.com/ktmeaton/plague-phylogeography/commit/2db7ec53) fix credits spacing
+* [```f51e071f```](https://github.com/ktmeaton/plague-phylogeography/commit/f51e071f) test iqtree model param
+* [```321419be```](https://github.com/ktmeaton/plague-phylogeography/commit/321419be) allow sra path to run parallel for biosample, add model param to iqtree
+* [```09326d2c```](https://github.com/ktmeaton/plague-phylogeography/commit/09326d2c) change sra metadata to biosample, add iqtree model param, fix time default max
+* [```b224464d```](https://github.com/ktmeaton/plague-phylogeography/commit/b224464d) update docs README
+* [```7cea6feb```](https://github.com/ktmeaton/plague-phylogeography/commit/7cea6feb) further reduce timeout to 60 min
+* [```61fb5879```](https://github.com/ktmeaton/plague-phylogeography/commit/61fb5879) constraint maxForks to specified maxForks
+* [```1a8a74e3```](https://github.com/ktmeaton/plague-phylogeography/commit/1a8a74e3) new terminal output for v0.1.4
+* [```487ec9e4```](https://github.com/ktmeaton/plague-phylogeography/commit/487ec9e4) reoptimize for parallel cluster
+* [```012c1d99```](https://github.com/ktmeaton/plague-phylogeography/commit/012c1d99) fix tag for snippy_pairwise
+* [```63b9611f```](https://github.com/ktmeaton/plague-phylogeography/commit/63b9611f) load all caches for compatibility with install script
+* [```602f7ca7```](https://github.com/ktmeaton/plague-phylogeography/commit/602f7ca7) try sra with new install script
+* [```f742a39e```](https://github.com/ktmeaton/plague-phylogeography/commit/f742a39e) remove references to step id
+* [```3db57139```](https://github.com/ktmeaton/plague-phylogeography/commit/3db57139) test assembly with new install script
+* [```8cbc9ae7```](https://github.com/ktmeaton/plague-phylogeography/commit/8cbc9ae7) add check cache
+* [```3185aeb0```](https://github.com/ktmeaton/plague-phylogeography/commit/3185aeb0) consolidate test env step
+* [```16225672```](https://github.com/ktmeaton/plague-phylogeography/commit/16225672) don't depend on install script
+* [```b8245fa8```](https://github.com/ktmeaton/plague-phylogeography/commit/b8245fa8) try install workflow with simplified script
+* [```71bed77d```](https://github.com/ktmeaton/plague-phylogeography/commit/71bed77d) check conda env before trying to create
+* [```0315666d```](https://github.com/ktmeaton/plague-phylogeography/commit/0315666d) conda env checking before uninstall
+* [```85a57fd2```](https://github.com/ktmeaton/plague-phylogeography/commit/85a57fd2) fix REPO capitals
+* [```6db86a2a```](https://github.com/ktmeaton/plague-phylogeography/commit/6db86a2a) fix bad command if check
+* [```a3b8d334```](https://github.com/ktmeaton/plague-phylogeography/commit/a3b8d334) use file check rather than ls
+* [```e6189792```](https://github.com/ktmeaton/plague-phylogeography/commit/e6189792) try catch for uninstalled files
+* [```e2128d5b```](https://github.com/ktmeaton/plague-phylogeography/commit/e2128d5b) better placed env var
+* [```1039498f```](https://github.com/ktmeaton/plague-phylogeography/commit/1039498f) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```b382795d```](https://github.com/ktmeaton/plague-phylogeography/commit/b382795d) better env catch and make uninstall generic
+* [```20394da6```](https://github.com/ktmeaton/plague-phylogeography/commit/20394da6) update docs README
+* [```517d2680```](https://github.com/ktmeaton/plague-phylogeography/commit/517d2680) Merge assembly missing data typo change
+* [```0d1a9ea8```](https://github.com/ktmeaton/plague-phylogeography/commit/0d1a9ea8) make install more generic
+* [```4fb51959```](https://github.com/ktmeaton/plague-phylogeography/commit/4fb51959) Fix typo in missing data
+* [```dadff422```](https://github.com/ktmeaton/plague-phylogeography/commit/dadff422) update docs README
+* [```131c26a7```](https://github.com/ktmeaton/plague-phylogeography/commit/131c26a7) simplify install instructions
+* [```671ecc31```](https://github.com/ktmeaton/plague-phylogeography/commit/671ecc31) try out missing data
+* [```665690e0```](https://github.com/ktmeaton/plague-phylogeography/commit/665690e0) update steps and exec mode
+* [```027b2875```](https://github.com/ktmeaton/plague-phylogeography/commit/027b2875) typo consistency
+* [```692633c9```](https://github.com/ktmeaton/plague-phylogeography/commit/692633c9) test run support and independent runs
+* [```40274edb```](https://github.com/ktmeaton/plague-phylogeography/commit/40274edb) add new optional iqtree output for support and runs
+* [```90aa13f6```](https://github.com/ktmeaton/plague-phylogeography/commit/90aa13f6) shorten timeout
+* [```a2aa94f0```](https://github.com/ktmeaton/plague-phylogeography/commit/a2aa94f0) add install and uninstall scripts
+* [```bdc69098```](https://github.com/ktmeaton/plague-phylogeography/commit/bdc69098) remove for_ prefix
+* [```cd2113ee```](https://github.com/ktmeaton/plague-phylogeography/commit/cd2113ee) update docstrings remove unnecessary for_ prefix
+* [```ec7386d4```](https://github.com/ktmeaton/plague-phylogeography/commit/ec7386d4) remove jackknifing
+* [```e074b7dc```](https://github.com/ktmeaton/plague-phylogeography/commit/e074b7dc) try 3 datasets instead of 4
+* [```9f73566f```](https://github.com/ktmeaton/plague-phylogeography/commit/9f73566f) add failsafe dataset limiter
+* [```543c2490```](https://github.com/ktmeaton/plague-phylogeography/commit/543c2490) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```19adaf99```](https://github.com/ktmeaton/plague-phylogeography/commit/19adaf99) remove debug echo statements
+* [```17acddfd```](https://github.com/ktmeaton/plague-phylogeography/commit/17acddfd) update docs README
+* [```2a46bfef```](https://github.com/ktmeaton/plague-phylogeography/commit/2a46bfef) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```f0950539```](https://github.com/ktmeaton/plague-phylogeography/commit/f0950539) reinstate update check
+* [```ce88dc66```](https://github.com/ktmeaton/plague-phylogeography/commit/ce88dc66) update docs README
+* [```3de043ca```](https://github.com/ktmeaton/plague-phylogeography/commit/3de043ca) debug echo statements
+* [```dc9e96fd```](https://github.com/ktmeaton/plague-phylogeography/commit/dc9e96fd) update conda install and eager install
+* [```c845923c```](https://github.com/ktmeaton/plague-phylogeography/commit/c845923c) test getting readme update
+* [```2d36f5aa```](https://github.com/ktmeaton/plague-phylogeography/commit/2d36f5aa) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```e6148f6c```](https://github.com/ktmeaton/plague-phylogeography/commit/e6148f6c) rerun pipelines with new cache names
+* [```427d1ed0```](https://github.com/ktmeaton/plague-phylogeography/commit/427d1ed0) hide toc make readme home page
+* [```ab9955ef```](https://github.com/ktmeaton/plague-phylogeography/commit/ab9955ef) update docs README
+* [```24c1db36```](https://github.com/ktmeaton/plague-phylogeography/commit/24c1db36) force commiting and pushing
+* [```86eee3b9```](https://github.com/ktmeaton/plague-phylogeography/commit/86eee3b9) don't check for file update
+* [```25bc66a6```](https://github.com/ktmeaton/plague-phylogeography/commit/25bc66a6) put update output in if statement
+* [```bdcedfac```](https://github.com/ktmeaton/plague-phylogeography/commit/bdcedfac) rebuild env cache with new names
+* [```b08b7060```](https://github.com/ktmeaton/plague-phylogeography/commit/b08b7060) remove wrong markdown README
+* [```1f00571b```](https://github.com/ktmeaton/plague-phylogeography/commit/1f00571b) remove wrong markdown README
+* [```79747512```](https://github.com/ktmeaton/plague-phylogeography/commit/79747512) test skipping outgroup download
+* [```e2c6a493```](https://github.com/ktmeaton/plague-phylogeography/commit/e2c6a493) only commit readme if updated
+* [```73a8aabf```](https://github.com/ktmeaton/plague-phylogeography/commit/73a8aabf) force adding the docs README
+* [```b569b703```](https://github.com/ktmeaton/plague-phylogeography/commit/b569b703) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```db7ed4d1```](https://github.com/ktmeaton/plague-phylogeography/commit/db7ed4d1) ignore docs/README.rst
+* [```35a22225```](https://github.com/ktmeaton/plague-phylogeography/commit/35a22225) try not wrapping mem in single quotes
+* [```5aae865f```](https://github.com/ktmeaton/plague-phylogeography/commit/5aae865f) fix artifact name
+* [```6b9191fa```](https://github.com/ktmeaton/plague-phylogeography/commit/6b9191fa) update docs README
+* [```55889900```](https://github.com/ktmeaton/plague-phylogeography/commit/55889900) test pushing new README
+* [```159c0bef```](https://github.com/ktmeaton/plague-phylogeography/commit/159c0bef) move README.rst into docs folder
+* [```29a99ef2```](https://github.com/ktmeaton/plague-phylogeography/commit/29a99ef2) disable multiple runs temp
+* [```a61140c1```](https://github.com/ktmeaton/plague-phylogeography/commit/a61140c1) disable multiple runs temp
+* [```c7ae27ff```](https://github.com/ktmeaton/plague-phylogeography/commit/c7ae27ff) reformat docs and linting to organize
+* [```f872cd46```](https://github.com/ktmeaton/plague-phylogeography/commit/f872cd46) rename cache restore id
+* [```42331f85```](https://github.com/ktmeaton/plague-phylogeography/commit/42331f85) add resume to the longTest
+* [```14ab311e```](https://github.com/ktmeaton/plague-phylogeography/commit/14ab311e) add 2 hour timeout limit
+* [```68a0f944```](https://github.com/ktmeaton/plague-phylogeography/commit/68a0f944) force 30 min timeout
+* [```ae9e0e3b```](https://github.com/ktmeaton/plague-phylogeography/commit/ae9e0e3b) add a long test and change artifacts to long
+* [```27cd6c83```](https://github.com/ktmeaton/plague-phylogeography/commit/27cd6c83) remove hardcode repository name
+* [```98030842```](https://github.com/ktmeaton/plague-phylogeography/commit/98030842) add back in the conda env var
+* [```b3ce4efc```](https://github.com/ktmeaton/plague-phylogeography/commit/b3ce4efc) fix conditional path
+* [```89872414```](https://github.com/ktmeaton/plague-phylogeography/commit/89872414) use github sha and proper hash
+* [```b6d53faa```](https://github.com/ktmeaton/plague-phylogeography/commit/b6d53faa) check conda env and fix hash file
+* [```f1175699```](https://github.com/ktmeaton/plague-phylogeography/commit/f1175699) split workflows, fail assembly if cache not restored
+* [```c1c102bd```](https://github.com/ktmeaton/plague-phylogeography/commit/c1c102bd) change cache restore step id
+* [```9b9aafff```](https://github.com/ktmeaton/plague-phylogeography/commit/9b9aafff) add conda cache restore to assembly pipeline
+* [```280abf5c```](https://github.com/ktmeaton/plague-phylogeography/commit/280abf5c) fix typo and add artifacts
+* [```55fca105```](https://github.com/ktmeaton/plague-phylogeography/commit/55fca105) add conda setup
+* [```c31f40ca```](https://github.com/ktmeaton/plague-phylogeography/commit/c31f40ca) add assembly pipeline to cache test
+* [```abd52711```](https://github.com/ktmeaton/plague-phylogeography/commit/abd52711) test global install again
+* [```3ab19df3```](https://github.com/ktmeaton/plague-phylogeography/commit/3ab19df3) add the conda env paths
+* [```17c20420```](https://github.com/ktmeaton/plague-phylogeography/commit/17c20420) incorporate plague-phylo cache
+* [```76464401```](https://github.com/ktmeaton/plague-phylogeography/commit/76464401) echo statements to test nextstrain
+* [```13b70a4e```](https://github.com/ktmeaton/plague-phylogeography/commit/13b70a4e) add env var for phylo and nextstrain
+* [```c7399609```](https://github.com/ktmeaton/plague-phylogeography/commit/c7399609) don't install auspice globally
+* [```52fa9749```](https://github.com/ktmeaton/plague-phylogeography/commit/52fa9749) test load and add nextstrain install
+* [```d25698cb```](https://github.com/ktmeaton/plague-phylogeography/commit/d25698cb) fix nextflow channel and add phylo install and test
+* [```12239d5a```](https://github.com/ktmeaton/plague-phylogeography/commit/12239d5a) add downloading phylo pipeline
+* [```364870fa```](https://github.com/ktmeaton/plague-phylogeography/commit/364870fa) version match eager nf
+* [```9595d586```](https://github.com/ktmeaton/plague-phylogeography/commit/9595d586) test loading eager env cache
+* [```23b5bbb7```](https://github.com/ktmeaton/plague-phylogeography/commit/23b5bbb7) move eager env file to github workspace
+* [```3b3e77f3```](https://github.com/ktmeaton/plague-phylogeography/commit/3b3e77f3) use an absolute path for hashfiles env
+* [```0ad76350```](https://github.com/ktmeaton/plague-phylogeography/commit/0ad76350) test cache eager env
+* [```ab082d92```](https://github.com/ktmeaton/plague-phylogeography/commit/ab082d92) add cache-test id
+* [```2b0eb188```](https://github.com/ktmeaton/plague-phylogeography/commit/2b0eb188) don't create or install if cache hit
+* [```ef4789b2```](https://github.com/ktmeaton/plague-phylogeography/commit/ef4789b2) check test env pre
+* [```86237ca5```](https://github.com/ktmeaton/plague-phylogeography/commit/86237ca5) retry cache load
+* [```d859530f```](https://github.com/ktmeaton/plague-phylogeography/commit/d859530f) try to load env cache without exclude dir
+* [```1741ebd3```](https://github.com/ktmeaton/plague-phylogeography/commit/1741ebd3) try to load env cache
+* [```40ecb628```](https://github.com/ktmeaton/plague-phylogeography/commit/40ecb628) try to cache env rather than pkgs
+* [```5cbc3651```](https://github.com/ktmeaton/plague-phylogeography/commit/5cbc3651) make conda envs path a global var
+* [```889d18bb```](https://github.com/ktmeaton/plague-phylogeography/commit/889d18bb) change env path after setup
+* [```82425bd3```](https://github.com/ktmeaton/plague-phylogeography/commit/82425bd3) change env path before setup
+* [```4dc71ef5```](https://github.com/ktmeaton/plague-phylogeography/commit/4dc71ef5) check env location
+* [```70747a28```](https://github.com/ktmeaton/plague-phylogeography/commit/70747a28) try to load cache
+* [```4935db41```](https://github.com/ktmeaton/plague-phylogeography/commit/4935db41) hardcode conda path
+* [```cbe22a86```](https://github.com/ktmeaton/plague-phylogeography/commit/cbe22a86) try conda path as var
+* [```e26d2812```](https://github.com/ktmeaton/plague-phylogeography/commit/e26d2812) test2 with local cache dir
+* [```d7a17792```](https://github.com/ktmeaton/plague-phylogeography/commit/d7a17792) minimal test env
+* [```ea47cb74```](https://github.com/ktmeaton/plague-phylogeography/commit/ea47cb74) try to cache after conda setup
+* [```625dc7e3```](https://github.com/ktmeaton/plague-phylogeography/commit/625dc7e3) now test if cache loads
+* [```b503cfa2```](https://github.com/ktmeaton/plague-phylogeography/commit/b503cfa2) checkout repo to get hash env
+* [```0147a4d4```](https://github.com/ktmeaton/plague-phylogeography/commit/0147a4d4) hash env file into cache name
+* [```f3a28a5a```](https://github.com/ktmeaton/plague-phylogeography/commit/f3a28a5a) hash env file into cache name
+* [```11a8ffcf```](https://github.com/ktmeaton/plague-phylogeography/commit/11a8ffcf) better cache name
+* [```f482e9b5```](https://github.com/ktmeaton/plague-phylogeography/commit/f482e9b5) test caching
+* [```93e97344```](https://github.com/ktmeaton/plague-phylogeography/commit/93e97344) test plain without cache
+* [```78f12de6```](https://github.com/ktmeaton/plague-phylogeography/commit/78f12de6) stop before snippy multi
+* [```8d56c800```](https://github.com/ktmeaton/plague-phylogeography/commit/8d56c800) add env links
+* [```d45b13b8```](https://github.com/ktmeaton/plague-phylogeography/commit/d45b13b8) attempt npm cache
+* [```ee33c6f3```](https://github.com/ktmeaton/plague-phylogeography/commit/ee33c6f3) fix param line end typo
+* [```434a210b```](https://github.com/ktmeaton/plague-phylogeography/commit/434a210b) add full pipeline
+* [```67002d96```](https://github.com/ktmeaton/plague-phylogeography/commit/67002d96) update description
+* [```18809cde```](https://github.com/ktmeaton/plague-phylogeography/commit/18809cde) add alrt and jackknife to branch support opt
+* [```5ea5c16f```](https://github.com/ktmeaton/plague-phylogeography/commit/5ea5c16f) update artifact paths
+* [```ba5dd5ea```](https://github.com/ktmeaton/plague-phylogeography/commit/ba5dd5ea) update artifact paths
+* [```345852bb```](https://github.com/ktmeaton/plague-phylogeography/commit/345852bb) troubleshoot missing artifact paths
+* [```c63cadc6```](https://github.com/ktmeaton/plague-phylogeography/commit/c63cadc6) fix param typos in eager process
+* [```77d3cd03```](https://github.com/ktmeaton/plague-phylogeography/commit/77d3cd03) run everything max resources param
+* [```5d3dc45d```](https://github.com/ktmeaton/plague-phylogeography/commit/5d3dc45d) test echo of dedupbam
+* [```379943b0```](https://github.com/ktmeaton/plague-phylogeography/commit/379943b0) test ls of dedupbam
+* [```3b2a3979```](https://github.com/ktmeaton/plague-phylogeography/commit/3b2a3979) comment out dedup rename
+* [```90daac81```](https://github.com/ktmeaton/plague-phylogeography/commit/90daac81) test eager cmd with dedup rename
+* [```09b9caa4```](https://github.com/ktmeaton/plague-phylogeography/commit/09b9caa4) upload conda export as artifact
+* [```759a9c49```](https://github.com/ktmeaton/plague-phylogeography/commit/759a9c49) add a conda list export each activate
+* [```f5303af5```](https://github.com/ktmeaton/plague-phylogeography/commit/f5303af5) try sra workflow as phylo cmd
+* [```a37465b8```](https://github.com/ktmeaton/plague-phylogeography/commit/a37465b8) parameterize eager var
+* [```6f2fc882```](https://github.com/ktmeaton/plague-phylogeography/commit/6f2fc882) revert back to plain eager test cmd
+* [```806c583c```](https://github.com/ktmeaton/plague-phylogeography/commit/806c583c) add proper conda activate
+* [```4ec5ed2f```](https://github.com/ktmeaton/plague-phylogeography/commit/4ec5ed2f) try vt install with 2015 label ver
+* [```c6636e9b```](https://github.com/ktmeaton/plague-phylogeography/commit/c6636e9b) install workflow won't depend on main pipeline
+* [```0255718a```](https://github.com/ktmeaton/plague-phylogeography/commit/0255718a) reinstate snippy command and remove reference dir output
+* [```a14a4cae```](https://github.com/ktmeaton/plague-phylogeography/commit/a14a4cae) vt before snippy install
+* [```140bd079```](https://github.com/ktmeaton/plague-phylogeography/commit/140bd079) fix broken vt dependncy to 0.57721
+* [```988d9ed6```](https://github.com/ktmeaton/plague-phylogeography/commit/988d9ed6) add more logging at start
+* [```8a09fb6f```](https://github.com/ktmeaton/plague-phylogeography/commit/8a09fb6f) sra cache path to launchdir
+* [```d5e67b17```](https://github.com/ktmeaton/plague-phylogeography/commit/d5e67b17) clean up old config
+* [```f9134821```](https://github.com/ktmeaton/plague-phylogeography/commit/f9134821) limit the assembly ftp opens
+* [```aa5707a3```](https://github.com/ktmeaton/plague-phylogeography/commit/aa5707a3) better specify resources
+* [```d2d82e19```](https://github.com/ktmeaton/plague-phylogeography/commit/d2d82e19) try to integrate eager back into regular pipeline
+* [```88ad99f6```](https://github.com/ktmeaton/plague-phylogeography/commit/88ad99f6) remove bam discad unmapped from eager param
+* [```b7741ba4```](https://github.com/ktmeaton/plague-phylogeography/commit/b7741ba4) add eager profile for github actions
+* [```b7a5a620```](https://github.com/ktmeaton/plague-phylogeography/commit/b7a5a620) add eager profile for github actions
+* [```f09d1086```](https://github.com/ktmeaton/plague-phylogeography/commit/f09d1086) publish snippy reference folder for debug
+* [```75d7ff72```](https://github.com/ktmeaton/plague-phylogeography/commit/75d7ff72) remove param to discard unmapped
+* [```adc6c0b0```](https://github.com/ktmeaton/plague-phylogeography/commit/adc6c0b0) adjust pairwise artifact and add ls check
+* [```baa5d256```](https://github.com/ktmeaton/plague-phylogeography/commit/baa5d256) update workflow title
+* [```2d92b1f2```](https://github.com/ktmeaton/plague-phylogeography/commit/2d92b1f2) upload snippy artifact
+* [```d42360ae```](https://github.com/ktmeaton/plague-phylogeography/commit/d42360ae) end before snippy multi
+* [```5b191fb9```](https://github.com/ktmeaton/plague-phylogeography/commit/5b191fb9) convert old pipeline workflow to just sra
+* [```b86adafb```](https://github.com/ktmeaton/plague-phylogeography/commit/b86adafb) create workflow just for testing assembly datasets
+* [```9a63c9b0```](https://github.com/ktmeaton/plague-phylogeography/commit/9a63c9b0) update treetime docs with jupyter notebook
+* [```b6996a1c```](https://github.com/ktmeaton/plague-phylogeography/commit/b6996a1c) specify eager ver as var
+* [```d016c383```](https://github.com/ktmeaton/plague-phylogeography/commit/d016c383) update ver to 0.1.4
+* [```5f667527```](https://github.com/ktmeaton/plague-phylogeography/commit/5f667527) allow X char for ambig as well
+* [```5107ae3c```](https://github.com/ktmeaton/plague-phylogeography/commit/5107ae3c) tidy help docs
+* [```359f6b8b```](https://github.com/ktmeaton/plague-phylogeography/commit/359f6b8b) add colorbar to rate variation
+* [```9d5c8a7d```](https://github.com/ktmeaton/plague-phylogeography/commit/9d5c8a7d) successful rate variation tree plot
+* [```94a34eeb```](https://github.com/ktmeaton/plague-phylogeography/commit/94a34eeb) finish rtt working on tree plotting
+* [```72e69e50```](https://github.com/ktmeaton/plague-phylogeography/commit/72e69e50) ignore notebook file output
+* [```c6e5364d```](https://github.com/ktmeaton/plague-phylogeography/commit/c6e5364d) separate notebook for full (rtt) analysis)
+* [```28c45e11```](https://github.com/ktmeaton/plague-phylogeography/commit/28c45e11) simply notebooks
+* [```7577cb21```](https://github.com/ktmeaton/plague-phylogeography/commit/7577cb21) new notebook for mugration and node dating
+* [```bfc5e8ae```](https://github.com/ktmeaton/plague-phylogeography/commit/bfc5e8ae) try vary rate and covary
+* [```266004ff```](https://github.com/ktmeaton/plague-phylogeography/commit/266004ff) jupyter notebook dependencies
+* [```32a64495```](https://github.com/ktmeaton/plague-phylogeography/commit/32a64495) extend plotting and export for treetime clock
+* [```e22b53ed```](https://github.com/ktmeaton/plague-phylogeography/commit/e22b53ed) notes about nwk convert
+* [```555e359c```](https://github.com/ktmeaton/plague-phylogeography/commit/555e359c) add skyline plotting
+* [```cef2bc1c```](https://github.com/ktmeaton/plague-phylogeography/commit/cef2bc1c) clock testings jupyter notebook
+* [```c35abda4```](https://github.com/ktmeaton/plague-phylogeography/commit/c35abda4) add timeout config to sra_download
+* [```e04a6463```](https://github.com/ktmeaton/plague-phylogeography/commit/e04a6463) reduce test cpus to 2
+* [```cdfce459```](https://github.com/ktmeaton/plague-phylogeography/commit/cdfce459) update ori subtree docs
+* [```afc51e97```](https://github.com/ktmeaton/plague-phylogeography/commit/afc51e97) add jupyter notebooks for test plotting
+* [```913de12b```](https://github.com/ktmeaton/plague-phylogeography/commit/913de12b) update exhibit doc
+* [```23ff447e```](https://github.com/ktmeaton/plague-phylogeography/commit/23ff447e) fix typo and limit memory
+* [```8b8d7fe6```](https://github.com/ktmeaton/plague-phylogeography/commit/8b8d7fe6) create the ncbi dir if it doesn't exist
+* [```623c356e```](https://github.com/ktmeaton/plague-phylogeography/commit/623c356e) fix file checking for sra config
+* [```c040d1bc```](https://github.com/ktmeaton/plague-phylogeography/commit/c040d1bc) add correct new version with new palette
+* [```57053489```](https://github.com/ktmeaton/plague-phylogeography/commit/57053489) revert copy json
+* [```d5e4d71f```](https://github.com/ktmeaton/plague-phylogeography/commit/d5e4d71f) update color palette
+* [```0e6fcd63```](https://github.com/ktmeaton/plague-phylogeography/commit/0e6fcd63) more muted blue
+* [```ab5603b4```](https://github.com/ktmeaton/plague-phylogeography/commit/ab5603b4) add config file for sra_download
+* [```5bfe1721```](https://github.com/ktmeaton/plague-phylogeography/commit/5bfe1721) fix hex typo
+* [```e038c89f```](https://github.com/ktmeaton/plague-phylogeography/commit/e038c89f) brighter blue for ORI
+* [```97b73cb9```](https://github.com/ktmeaton/plague-phylogeography/commit/97b73cb9) color palette change qual
+* [```e4ec1fee```](https://github.com/ktmeaton/plague-phylogeography/commit/e4ec1fee) reinstate Algeria3 biovar
+* [```5421e69a```](https://github.com/ktmeaton/plague-phylogeography/commit/5421e69a) fix biovar typo
+* [```cdeee94e```](https://github.com/ktmeaton/plague-phylogeography/commit/cdeee94e) remove biovar info Algeria3
+* [```3f84e72d```](https://github.com/ktmeaton/plague-phylogeography/commit/3f84e72d) add biovar color map rainbow
+* [```ce2a919f```](https://github.com/ktmeaton/plague-phylogeography/commit/ce2a919f) update biovars for CIS
+* [```bbbc382c```](https://github.com/ktmeaton/plague-phylogeography/commit/bbbc382c) troubleshooting error message
+* [```8028b3ab```](https://github.com/ktmeaton/plague-phylogeography/commit/8028b3ab) mkdir param catch
+* [```74c0fbfc```](https://github.com/ktmeaton/plague-phylogeography/commit/74c0fbfc) run sra_download before eager test
+* [```db4bd630```](https://github.com/ktmeaton/plague-phylogeography/commit/db4bd630) currently functioning nextstrain section
+* [```9dff87ae```](https://github.com/ktmeaton/plague-phylogeography/commit/9dff87ae) put geopy explicitly as pip install
+* [```876346b3```](https://github.com/ktmeaton/plague-phylogeography/commit/876346b3) fix ref and metadata path
+* [```d33f4e70```](https://github.com/ktmeaton/plague-phylogeography/commit/d33f4e70) add nextstrain install
+* [```c4d75d37```](https://github.com/ktmeaton/plague-phylogeography/commit/c4d75d37) remove pestoides biovar fix nepal geo
+* [```89bdd78e```](https://github.com/ktmeaton/plague-phylogeography/commit/89bdd78e) new clade MED-ANT split
+* [```98a52782```](https://github.com/ktmeaton/plague-phylogeography/commit/98a52782) fix bp error
+* [```059b460a```](https://github.com/ktmeaton/plague-phylogeography/commit/059b460a) add med antiqua mrca clade
+* [```30e02e06```](https://github.com/ktmeaton/plague-phylogeography/commit/30e02e06) add the caf1 genes
+* [```c057c861```](https://github.com/ktmeaton/plague-phylogeography/commit/c057c861) add modern assembly auspice dataset
+* [```2068e3a3```](https://github.com/ktmeaton/plague-phylogeography/commit/2068e3a3) test clades pandemic
+* [```3be246df```](https://github.com/ktmeaton/plague-phylogeography/commit/3be246df) fix country geocode errors
+* [```c1e54635```](https://github.com/ktmeaton/plague-phylogeography/commit/c1e54635) rename clades extension
+* [```61d14718```](https://github.com/ktmeaton/plague-phylogeography/commit/61d14718) add the psaC clade
+* [```bd69e23f```](https://github.com/ktmeaton/plague-phylogeography/commit/bd69e23f) remove excess print statement
+* [```e8f4012a```](https://github.com/ktmeaton/plague-phylogeography/commit/e8f4012a) tidy install
+* [```09842871```](https://github.com/ktmeaton/plague-phylogeography/commit/09842871) add clades and gene reconstruct
+* [```d097408b```](https://github.com/ktmeaton/plague-phylogeography/commit/d097408b) add state geo resolution
+* [```f41198ad```](https://github.com/ktmeaton/plague-phylogeography/commit/f41198ad) fix no data char geocode
+* [```18e9bd38```](https://github.com/ktmeaton/plague-phylogeography/commit/18e9bd38) switch biovar to reconstruct var
+* [```d8885002```](https://github.com/ktmeaton/plague-phylogeography/commit/d8885002) change time dist measure
+* [```354c4eaf```](https://github.com/ktmeaton/plague-phylogeography/commit/354c4eaf) delimiter fix
+* [```d2489cfe```](https://github.com/ktmeaton/plague-phylogeography/commit/d2489cfe) new config for modern assemblies
+* [```2f6e97e1```](https://github.com/ktmeaton/plague-phylogeography/commit/2f6e97e1) update format Assembly metadata
+* [```a10bd2c5```](https://github.com/ktmeaton/plague-phylogeography/commit/a10bd2c5) doc update for new geocode
+* [```407d6075```](https://github.com/ktmeaton/plague-phylogeography/commit/407d6075) doc update for new geocode
+* [```34f49533```](https://github.com/ktmeaton/plague-phylogeography/commit/34f49533) try geopy in nextstrain env
+* [```6d4dfcad```](https://github.com/ktmeaton/plague-phylogeography/commit/6d4dfcad) update georeferencing
+* [```6d5daef6```](https://github.com/ktmeaton/plague-phylogeography/commit/6d5daef6) remove test env suffix
+* [```9fb57024```](https://github.com/ktmeaton/plague-phylogeography/commit/9fb57024) update nextstrain env instructions
+* [```b717a4cf```](https://github.com/ktmeaton/plague-phylogeography/commit/b717a4cf) fix config dir for yaml files
+* [```cfd56313```](https://github.com/ktmeaton/plague-phylogeography/commit/cfd56313) update master table db
+* [```e8f468eb```](https://github.com/ktmeaton/plague-phylogeography/commit/e8f468eb) complete geo and date
+* [```3afb8833```](https://github.com/ktmeaton/plague-phylogeography/commit/3afb8833) fixing up georgian geo
+* [```3c6f5a19```](https://github.com/ktmeaton/plague-phylogeography/commit/3c6f5a19) all but missing geo
+* [```742c665d```](https://github.com/ktmeaton/plague-phylogeography/commit/742c665d) complete Peru geo
+* [```51d470d5```](https://github.com/ktmeaton/plague-phylogeography/commit/51d470d5) treetime json scripts
+* [```576fc7a3```](https://github.com/ktmeaton/plague-phylogeography/commit/576fc7a3) test fusing treetime and augur
+* [```a14ad4ab```](https://github.com/ktmeaton/plague-phylogeography/commit/a14ad4ab) update exhibit for no outgroup
+* [```97e57e1b```](https://github.com/ktmeaton/plague-phylogeography/commit/97e57e1b) finished India metadata
+* [```2a9600d6```](https://github.com/ktmeaton/plague-phylogeography/commit/2a9600d6) finish armenia azerbaijan
+* [```2e3afd3d```](https://github.com/ktmeaton/plague-phylogeography/commit/2e3afd3d) save before eroshenko reconcile
+* [```4b712824```](https://github.com/ktmeaton/plague-phylogeography/commit/4b712824) subdivide geo location into types
+* [```2ef90a99```](https://github.com/ktmeaton/plague-phylogeography/commit/2ef90a99) work on updating anti-plague institute metadata
+* [```1eb29983```](https://github.com/ktmeaton/plague-phylogeography/commit/1eb29983) add plague foci geocoding
+* [```e6cb7336```](https://github.com/ktmeaton/plague-phylogeography/commit/e6cb7336) fix sed target
+* [```78a29944```](https://github.com/ktmeaton/plague-phylogeography/commit/78a29944) sed in place
+* [```b5b652b7```](https://github.com/ktmeaton/plague-phylogeography/commit/b5b652b7) update db comments for low cov sample
+* [```f823a84e```](https://github.com/ktmeaton/plague-phylogeography/commit/f823a84e) change unknown and missing
+* [```70d3f755```](https://github.com/ktmeaton/plague-phylogeography/commit/70d3f755) new metadata format script Assembly
+* [```115fc1c2```](https://github.com/ktmeaton/plague-phylogeography/commit/115fc1c2) new metadata format script Assembly
+* [```f8b7370c```](https://github.com/ktmeaton/plague-phylogeography/commit/f8b7370c) add new install commands to pipeline workflow
+* [```4fc9add6```](https://github.com/ktmeaton/plague-phylogeography/commit/4fc9add6) db update full comments for BioSample
+* [```ad62451a```](https://github.com/ktmeaton/plague-phylogeography/commit/ad62451a) remove explicit sqlite param in cmd
+* [```f8ae0509```](https://github.com/ktmeaton/plague-phylogeography/commit/f8ae0509) add eager rev to help cmd
+* [```968efa54```](https://github.com/ktmeaton/plague-phylogeography/commit/968efa54) more comprehensive install test
+* [```32a19781```](https://github.com/ktmeaton/plague-phylogeography/commit/32a19781) test graphviz and eager separately
+* [```2da21fb9```](https://github.com/ktmeaton/plague-phylogeography/commit/2da21fb9) fix optimize typo
+* [```ce41a0de```](https://github.com/ktmeaton/plague-phylogeography/commit/ce41a0de) add SCDS2020 to showcase
+* [```55633271```](https://github.com/ktmeaton/plague-phylogeography/commit/55633271) add showcase section
+* [```6dfd8216```](https://github.com/ktmeaton/plague-phylogeography/commit/6dfd8216) try to fix rename loop
+* [```029fb8c2```](https://github.com/ktmeaton/plague-phylogeography/commit/029fb8c2) attempt to fix snippy dedup bam RG issue
+* [```25beda6e```](https://github.com/ktmeaton/plague-phylogeography/commit/25beda6e) correct max sra from 1 to 2
+* [```08772a1c```](https://github.com/ktmeaton/plague-phylogeography/commit/08772a1c) simplify pipeline
+* [```b9347ede```](https://github.com/ktmeaton/plague-phylogeography/commit/b9347ede) add config param iqtree_runs
+* [```c46c2c5c```](https://github.com/ktmeaton/plague-phylogeography/commit/c46c2c5c) fix branch support param
+* [```3cebf053```](https://github.com/ktmeaton/plague-phylogeography/commit/3cebf053) reduce testing assembly, disable branch support default
+* [```c3e54268```](https://github.com/ktmeaton/plague-phylogeography/commit/c3e54268) reducing testing and example to 1 iqtree run
+* [```2f7fbb37```](https://github.com/ktmeaton/plague-phylogeography/commit/2f7fbb37) rename phylo-env env
+* [```48ef9fc8```](https://github.com/ktmeaton/plague-phylogeography/commit/48ef9fc8) update environment name and tidy env
+* [```1f25f5b2```](https://github.com/ktmeaton/plague-phylogeography/commit/1f25f5b2) try launchdir not basedir for output
+* [```4f6ef192```](https://github.com/ktmeaton/plague-phylogeography/commit/4f6ef192) update output with time
+* [```366457f4```](https://github.com/ktmeaton/plague-phylogeography/commit/366457f4) use absolute link to logo
+* [```9f45476b```](https://github.com/ktmeaton/plague-phylogeography/commit/9f45476b) add logo
+* [```6b6b0ee2```](https://github.com/ktmeaton/plague-phylogeography/commit/6b6b0ee2) remove extra echo true
+* [```43d115a6```](https://github.com/ktmeaton/plague-phylogeography/commit/43d115a6) add license
+* [```7e7f2d1b```](https://github.com/ktmeaton/plague-phylogeography/commit/7e7f2d1b) update move and workflow
+* [```84a03380```](https://github.com/ktmeaton/plague-phylogeography/commit/84a03380) move config files to config dir
+* [```1e2c8528```](https://github.com/ktmeaton/plague-phylogeography/commit/1e2c8528) remove old annot files
+* [```1d7d3364```](https://github.com/ktmeaton/plague-phylogeography/commit/1d7d3364) correct iqtree param
+* [```637019dd```](https://github.com/ktmeaton/plague-phylogeography/commit/637019dd) update for default database
+* [```495ed417```](https://github.com/ktmeaton/plague-phylogeography/commit/495ed417) add more iqtree param
+* [```af33e640```](https://github.com/ktmeaton/plague-phylogeography/commit/af33e640) add more iqtree param
+* [```7caf6908```](https://github.com/ktmeaton/plague-phylogeography/commit/7caf6908) make sqlite parameter a default
+* [```52e8d5e9```](https://github.com/ktmeaton/plague-phylogeography/commit/52e8d5e9) set a default sqlite database to yp
+* [```cfa265e7```](https://github.com/ktmeaton/plague-phylogeography/commit/cfa265e7) add optional outgroup to iqtree
+* [```77ddfd32```](https://github.com/ktmeaton/plague-phylogeography/commit/77ddfd32) list conda env
+* [```021b9114```](https://github.com/ktmeaton/plague-phylogeography/commit/021b9114) mock of outgroup process for iqtree
+* [```369c52c3```](https://github.com/ktmeaton/plague-phylogeography/commit/369c52c3) fix environment name bug to phylo-dev
+* [```c5b35a16```](https://github.com/ktmeaton/plague-phylogeography/commit/c5b35a16) add conda activate statements
+* [```16371c24```](https://github.com/ktmeaton/plague-phylogeography/commit/16371c24) add process outgroup_download
+* [```31788beb```](https://github.com/ktmeaton/plague-phylogeography/commit/31788beb) make dynamic rng
+* [```19f6b6df```](https://github.com/ktmeaton/plague-phylogeography/commit/19f6b6df) add example output
+* [```240b76f4```](https://github.com/ktmeaton/plague-phylogeography/commit/240b76f4) update trigers with new main and environment
+* [```accb443e```](https://github.com/ktmeaton/plague-phylogeography/commit/accb443e) function snippy pairwise for fna
+* [```873ddbfd```](https://github.com/ktmeaton/plague-phylogeography/commit/873ddbfd) functional fna bam flatten collect
+* [```e2299c6d```](https://github.com/ktmeaton/plague-phylogeography/commit/e2299c6d) BROKEN adding bam to snippy pairwise
+* [```6e33611f```](https://github.com/ktmeaton/plague-phylogeography/commit/6e33611f) fix the terrible if statements back to when
+* [```4a2343ce```](https://github.com/ktmeaton/plague-phylogeography/commit/4a2343ce) put into all one job
+* [```54327a72```](https://github.com/ktmeaton/plague-phylogeography/commit/54327a72) fix sra typo spacing
+* [```c0362038```](https://github.com/ktmeaton/plague-phylogeography/commit/c0362038) fix typo and pipeline call
+* [```eef44c47```](https://github.com/ktmeaton/plague-phylogeography/commit/eef44c47) fix typo and pipeline call
+* [```06f73136```](https://github.com/ktmeaton/plague-phylogeography/commit/06f73136) condense pipeline to one workflow
+* [```02a082c1```](https://github.com/ktmeaton/plague-phylogeography/commit/02a082c1) put nf eager after plague phylo
+* [```d71767e8```](https://github.com/ktmeaton/plague-phylogeography/commit/d71767e8) condense and rename phylo-env to environment.yaml
+* [```91718233```](https://github.com/ktmeaton/plague-phylogeography/commit/91718233) pull nf eager in two steps
+* [```4195f443```](https://github.com/ktmeaton/plague-phylogeography/commit/4195f443) remove nf eager rev code
+* [```eb67aa54```](https://github.com/ktmeaton/plague-phylogeography/commit/eb67aa54) hard code rev nf eager
+* [```89530129```](https://github.com/ktmeaton/plague-phylogeography/commit/89530129) try to fix nf eager install
+* [```68e64987```](https://github.com/ktmeaton/plague-phylogeography/commit/68e64987) fix workflow typo
+* [```5fdb9d97```](https://github.com/ktmeaton/plague-phylogeography/commit/5fdb9d97) change install to nextflow pull
+* [```c3455905```](https://github.com/ktmeaton/plague-phylogeography/commit/c3455905) remove multiqc_config manual handling
+* [```7261e439```](https://github.com/ktmeaton/plague-phylogeography/commit/7261e439) remove eager multiqc_config manual
+* [```030e7778```](https://github.com/ktmeaton/plague-phylogeography/commit/030e7778) rename pipeline.nf to main.nf
+* [```e281284a```](https://github.com/ktmeaton/plague-phylogeography/commit/e281284a) fixed resume option for eager process
+* [```ee3b3441```](https://github.com/ktmeaton/plague-phylogeography/commit/ee3b3441) control eager rev as var
+* [```42fa26ad```](https://github.com/ktmeaton/plague-phylogeography/commit/42fa26ad) add graphviz to env
+* [```fa20b299```](https://github.com/ktmeaton/plague-phylogeography/commit/fa20b299) locally functioning eager with new work dir
+* [```bd6bd736```](https://github.com/ktmeaton/plague-phylogeography/commit/bd6bd736) new install instructions
+* [```a343b34c```](https://github.com/ktmeaton/plague-phylogeography/commit/a343b34c) add example output
+* [```672a5612```](https://github.com/ktmeaton/plague-phylogeography/commit/672a5612) move multiqic files to config dir
+* [```108a90a6```](https://github.com/ktmeaton/plague-phylogeography/commit/108a90a6) run eager test outside pipeline
+* [```331bf042```](https://github.com/ktmeaton/plague-phylogeography/commit/331bf042) remove eager for testing
+* [```14c076e1```](https://github.com/ktmeaton/plague-phylogeography/commit/14c076e1) test perl5lib setup
+* [```0826b537```](https://github.com/ktmeaton/plague-phylogeography/commit/0826b537) now testing assembly and sra together
+* [```3bcb1244```](https://github.com/ktmeaton/plague-phylogeography/commit/3bcb1244) echo PERL5LIB debug
+* [```1cf09d35```](https://github.com/ktmeaton/plague-phylogeography/commit/1cf09d35) remove old notes file
+* [```0257b2d9```](https://github.com/ktmeaton/plague-phylogeography/commit/0257b2d9) remove old nextstrain dir
+* [```076fa7e0```](https://github.com/ktmeaton/plague-phylogeography/commit/076fa7e0) remove eager dir
+* [```847d8d07```](https://github.com/ktmeaton/plague-phylogeography/commit/847d8d07) m2r update readme and upload html artifact
+* [```1ca39ff0```](https://github.com/ktmeaton/plague-phylogeography/commit/1ca39ff0) update README docs
+* [```207f650c```](https://github.com/ktmeaton/plague-phylogeography/commit/207f650c) edit modern assembly section
+* [```cd4d870c```](https://github.com/ktmeaton/plague-phylogeography/commit/cd4d870c) improve install and quick start
+* [```7f8392f3```](https://github.com/ktmeaton/plague-phylogeography/commit/7f8392f3) try installing nextflow into eager conda env
+* [```299b0fb8```](https://github.com/ktmeaton/plague-phylogeography/commit/299b0fb8) rearrange to optimze eager install
+* [```656a19d7```](https://github.com/ktmeaton/plague-phylogeography/commit/656a19d7) fix workflow errors
+* [```51cd334b```](https://github.com/ktmeaton/plague-phylogeography/commit/51cd334b) rearrange install nextflow first
+* [```cd46a590```](https://github.com/ktmeaton/plague-phylogeography/commit/cd46a590) attempt conda create with eager env
+* [```4f311994```](https://github.com/ktmeaton/plague-phylogeography/commit/4f311994) update eager env to dev 2.2.0
+* [```6bef53a4```](https://github.com/ktmeaton/plague-phylogeography/commit/6bef53a4) fix broken sra workflow rule
+* [```50d795ea```](https://github.com/ktmeaton/plague-phylogeography/commit/50d795ea) greatly simplify SRA pipeline instructions
+* [```54ae4dd5```](https://github.com/ktmeaton/plague-phylogeography/commit/54ae4dd5) have eager create conda env
+* [```b4936c65```](https://github.com/ktmeaton/plague-phylogeography/commit/b4936c65) add eager-env from dev
+* [```ba090411```](https://github.com/ktmeaton/plague-phylogeography/commit/ba090411) add eager to test workflow
+* [```c8dea94b```](https://github.com/ktmeaton/plague-phylogeography/commit/c8dea94b) move paper to new repository
+* [```673035d9```](https://github.com/ktmeaton/plague-phylogeography/commit/673035d9) new sra testing workflow
+* [```8f7c6d21```](https://github.com/ktmeaton/plague-phylogeography/commit/8f7c6d21) functioning sra download
+* [```75305708```](https://github.com/ktmeaton/plague-phylogeography/commit/75305708) large update and script bugfix
+* [```055124ff```](https://github.com/ktmeaton/plague-phylogeography/commit/055124ff) add D101 query to ncbimeta BioSample search
+* [```8a291d3d```](https://github.com/ktmeaton/plague-phylogeography/commit/8a291d3d) finished commenting Ancient projects round 1
+* [```bc5f7f42```](https://github.com/ktmeaton/plague-phylogeography/commit/bc5f7f42) update EAGER ancient comments and bioproject acc
+* [```072ecbf0```](https://github.com/ktmeaton/plague-phylogeography/commit/072ecbf0) add notes for all EAGER run
+* [```40c403d7```](https://github.com/ktmeaton/plague-phylogeography/commit/40c403d7) update the EAGER and KEEP comments
+* [```4fa33442```](https://github.com/ktmeaton/plague-phylogeography/commit/4fa33442) update directories
+* [```c38a60cd```](https://github.com/ktmeaton/plague-phylogeography/commit/c38a60cd) update directories
+* [```8c9d5c79```](https://github.com/ktmeaton/plague-phylogeography/commit/8c9d5c79) successful eager run test
+* [```297bc83a```](https://github.com/ktmeaton/plague-phylogeography/commit/297bc83a) add black and flake8
+* [```be906214```](https://github.com/ktmeaton/plague-phylogeography/commit/be906214) instructions for sra download
+* [```39c60bca```](https://github.com/ktmeaton/plague-phylogeography/commit/39c60bca) change sra download dir
+* [```a3adedc5```](https://github.com/ktmeaton/plague-phylogeography/commit/a3adedc5) change sra download dir
+* [```0a2b9607```](https://github.com/ktmeaton/plague-phylogeography/commit/0a2b9607) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```20ee84af```](https://github.com/ktmeaton/plague-phylogeography/commit/20ee84af) update eager tsv script
+* [```d48b56b3```](https://github.com/ktmeaton/plague-phylogeography/commit/d48b56b3) sra notes 8291
+* [```62033568```](https://github.com/ktmeaton/plague-phylogeography/commit/62033568) add outgroups ftp links
+* [```8cd7905c```](https://github.com/ktmeaton/plague-phylogeography/commit/8cd7905c) note add outgroup
+* [```1a2099e8```](https://github.com/ktmeaton/plague-phylogeography/commit/1a2099e8) Set theme jekyll-theme-cayman
+* [```92b2f52b```](https://github.com/ktmeaton/plague-phylogeography/commit/92b2f52b) Set theme jekyll-theme-dinky
+* [```ed413e3b```](https://github.com/ktmeaton/plague-phylogeography/commit/ed413e3b) add good debate lit sources
+* [```4eca9c25```](https://github.com/ktmeaton/plague-phylogeography/commit/4eca9c25) reorganize paper text
+* [```b9f9c1f4```](https://github.com/ktmeaton/plague-phylogeography/commit/b9f9c1f4) note about breaking up snippy
+* [```6e534e02```](https://github.com/ktmeaton/plague-phylogeography/commit/6e534e02) get artifacts from test outdir
+* [```64e22d64```](https://github.com/ktmeaton/plague-phylogeography/commit/64e22d64) remove eager from pipeline for now
+* [```591f1fb7```](https://github.com/ktmeaton/plague-phylogeography/commit/591f1fb7) add sql command select
+* [```940a2359```](https://github.com/ktmeaton/plague-phylogeography/commit/940a2359) reset ncbimeta pip conflicts pyyaml
+* [```01a52c41```](https://github.com/ktmeaton/plague-phylogeography/commit/01a52c41) allow img inline html
+* [```46f4753a```](https://github.com/ktmeaton/plague-phylogeography/commit/46f4753a) run pipeline if env yaml updates
+* [```70889acf```](https://github.com/ktmeaton/plague-phylogeography/commit/70889acf) switch ncbimeta to pip install
+* [```80294505```](https://github.com/ktmeaton/plague-phylogeography/commit/80294505) specify commit rev for eager pull
+* [```b0e7b913```](https://github.com/ktmeaton/plague-phylogeography/commit/b0e7b913) add assignee to other issues
+* [```c0a22389```](https://github.com/ktmeaton/plague-phylogeography/commit/c0a22389) lint CHANGELOG
+* [```407a244d```](https://github.com/ktmeaton/plague-phylogeography/commit/407a244d) add PR and issue templates
+* [```cb0d2687```](https://github.com/ktmeaton/plague-phylogeography/commit/cb0d2687) add pipeline steps move usage to rtd
+* [```d0d5d674```](https://github.com/ktmeaton/plague-phylogeography/commit/d0d5d674) add assembly pipeline
+* [```b9dd5f12```](https://github.com/ktmeaton/plague-phylogeography/commit/b9dd5f12) up to verify samples
+* [```06a9c22a```](https://github.com/ktmeaton/plague-phylogeography/commit/06a9c22a) fix headings level
+* [```98fe92dd```](https://github.com/ktmeaton/plague-phylogeography/commit/98fe92dd) overhaul section headers
+* [```083f1099```](https://github.com/ktmeaton/plague-phylogeography/commit/083f1099) document database curation
+* [```a4a56d74```](https://github.com/ktmeaton/plague-phylogeography/commit/a4a56d74) test sublist
+* [```245463df```](https://github.com/ktmeaton/plague-phylogeography/commit/245463df) remove treetime issue notes
+* [```2dcac55d```](https://github.com/ktmeaton/plague-phylogeography/commit/2dcac55d) remove old markdown config
+* [```66e20244```](https://github.com/ktmeaton/plague-phylogeography/commit/66e20244) remove old trace files
+* [```44896ad5```](https://github.com/ktmeaton/plague-phylogeography/commit/44896ad5) cleanup morelli and cui
+* [```60db533f```](https://github.com/ktmeaton/plague-phylogeography/commit/60db533f) test main render
+* [```b9ec0aec```](https://github.com/ktmeaton/plague-phylogeography/commit/b9ec0aec) update ncbimeta to v0.6.6
+* [```29219351```](https://github.com/ktmeaton/plague-phylogeography/commit/29219351) lint exhibit_link
+* [```b7362cee```](https://github.com/ktmeaton/plague-phylogeography/commit/b7362cee) lint README
+* [```cd31ea78```](https://github.com/ktmeaton/plague-phylogeography/commit/cd31ea78) lint main rst
+* [```4494e12e```](https://github.com/ktmeaton/plague-phylogeography/commit/4494e12e) lint README
+* [```63e2fc19```](https://github.com/ktmeaton/plague-phylogeography/commit/63e2fc19) lint README
+* [```f69ac024```](https://github.com/ktmeaton/plague-phylogeography/commit/f69ac024) lint README
 
 ## v0.1.3
 
 ### Commits
 
-* [```1c5e86a```](https://github.com/ktmeaton/plague-phylogeography/commit/1c5e86a) update to v0.1.3
-* [```012f491```](https://github.com/ktmeaton/plague-phylogeography/commit/012f491) fix typos
-* [```240cd82```](https://github.com/ktmeaton/plague-phylogeography/commit/240cd82) fix tree compare link
-* [```c1b059b```](https://github.com/ktmeaton/plague-phylogeography/commit/c1b059b) fix tree compare link
-* [```8b15cfe```](https://github.com/ktmeaton/plague-phylogeography/commit/8b15cfe) recording draft
-* [```96b161b```](https://github.com/ktmeaton/plague-phylogeography/commit/96b161b) update links
-* [```da9ca42```](https://github.com/ktmeaton/plague-phylogeography/commit/da9ca42) clean up status
-* [```6157e45```](https://github.com/ktmeaton/plague-phylogeography/commit/6157e45) ready for proofreading
-* [```bf11a24```](https://github.com/ktmeaton/plague-phylogeography/commit/bf11a24) up to interdisc
-* [```5226120```](https://github.com/ktmeaton/plague-phylogeography/commit/5226120) begin editing
-* [```3f7864a```](https://github.com/ktmeaton/plague-phylogeography/commit/3f7864a) remove test hrule
-* [```2f02c64```](https://github.com/ktmeaton/plague-phylogeography/commit/2f02c64) test hrule
-* [```676c108```](https://github.com/ktmeaton/plague-phylogeography/commit/676c108) first page color country
-* [```baf1ea0```](https://github.com/ktmeaton/plague-phylogeography/commit/baf1ea0) first page color country
-* [```aa32d33```](https://github.com/ktmeaton/plague-phylogeography/commit/aa32d33) draft up to publish
-* [```0af4add```](https://github.com/ktmeaton/plague-phylogeography/commit/0af4add) draft of playground
-* [```ef88220```](https://github.com/ktmeaton/plague-phylogeography/commit/ef88220) first two pages initial
-* [```03c8635```](https://github.com/ktmeaton/plague-phylogeography/commit/03c8635) fix single dataset
-* [```1ab3648```](https://github.com/ktmeaton/plague-phylogeography/commit/1ab3648) upload DHSI narrative
-* [```e23a79e```](https://github.com/ktmeaton/plague-phylogeography/commit/e23a79e) update cui2013 with new uncertainty param
-* [```ff0102d```](https://github.com/ktmeaton/plague-phylogeography/commit/ff0102d) date range temp fix
-* [```7507f3c```](https://github.com/ktmeaton/plague-phylogeography/commit/7507f3c) add nexus newick script
-* [```2761f9e```](https://github.com/ktmeaton/plague-phylogeography/commit/2761f9e) save before changing date format
-* [```ffd79c7```](https://github.com/ktmeaton/plague-phylogeography/commit/ffd79c7) new augur param for morelli
-* [```84d07ce```](https://github.com/ktmeaton/plague-phylogeography/commit/84d07ce) update morelli json
-* [```0c71664```](https://github.com/ktmeaton/plague-phylogeography/commit/0c71664) change date coloring and move files
-* [```e0c8c97```](https://github.com/ktmeaton/plague-phylogeography/commit/e0c8c97) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```03b5f05```](https://github.com/ktmeaton/plague-phylogeography/commit/03b5f05) remove Angola json auspice
-* [```d325bca```](https://github.com/ktmeaton/plague-phylogeography/commit/d325bca) simplify metadata section
-* [```fac540a```](https://github.com/ktmeaton/plague-phylogeography/commit/fac540a) put wildcard output first
-* [```819f234```](https://github.com/ktmeaton/plague-phylogeography/commit/819f234) fix snippy multi resume bug
-* [```adcf393```](https://github.com/ktmeaton/plague-phylogeography/commit/adcf393) note about fail to publish issue
-* [```b92fd6b```](https://github.com/ktmeaton/plague-phylogeography/commit/b92fd6b) REMOVE Angola strain
-* [```1fd8a68```](https://github.com/ktmeaton/plague-phylogeography/commit/1fd8a68) docs before disabling covariance
-* [```d98c046```](https://github.com/ktmeaton/plague-phylogeography/commit/d98c046) strain date interval
-* [```3d51094```](https://github.com/ktmeaton/plague-phylogeography/commit/3d51094) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```49f1855```](https://github.com/ktmeaton/plague-phylogeography/commit/49f1855) add cui 2013 treefile
-* [```ba70cd3```](https://github.com/ktmeaton/plague-phylogeography/commit/ba70cd3) export auspice copy command
-* [```3e0093a```](https://github.com/ktmeaton/plague-phylogeography/commit/3e0093a) add cui 2013 auspice files
-* [```4763fad```](https://github.com/ktmeaton/plague-phylogeography/commit/4763fad) add cui2013 auspice config
-* [```065e1c8```](https://github.com/ktmeaton/plague-phylogeography/commit/065e1c8) remove old unused auspice datasets
-* [```8690281```](https://github.com/ktmeaton/plague-phylogeography/commit/8690281) add auspice morelli
-* [```9652e12```](https://github.com/ktmeaton/plague-phylogeography/commit/9652e12) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```a52670f```](https://github.com/ktmeaton/plague-phylogeography/commit/a52670f) more labels for colorings
-* [```538ac31```](https://github.com/ktmeaton/plague-phylogeography/commit/538ac31) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```0e7c4a6```](https://github.com/ktmeaton/plague-phylogeography/commit/0e7c4a6) morelli updates
-* [```f7964bf```](https://github.com/ktmeaton/plague-phylogeography/commit/f7964bf) update auspice config morelli
-* [```f928064```](https://github.com/ktmeaton/plague-phylogeography/commit/f928064) standardize biovar med spelling
-* [```af0d9e5```](https://github.com/ktmeaton/plague-phylogeography/commit/af0d9e5) metadata prep complete
-* [```f4cfd1f```](https://github.com/ktmeaton/plague-phylogeography/commit/f4cfd1f) major cui annot and docs
-* [```b52db23```](https://github.com/ktmeaton/plague-phylogeography/commit/b52db23) begin adding cui docs
-* [```5f060ff```](https://github.com/ktmeaton/plague-phylogeography/commit/5f060ff) update cui and morelli host info
-* [```51f58e3```](https://github.com/ktmeaton/plague-phylogeography/commit/51f58e3) update before cui2013 run
-* [```d765bf5```](https://github.com/ktmeaton/plague-phylogeography/commit/d765bf5) augur trees and plots
-* [```0a32f38```](https://github.com/ktmeaton/plague-phylogeography/commit/0a32f38) notes on treetime vs augur refine
-* [```d778add```](https://github.com/ktmeaton/plague-phylogeography/commit/d778add) fixed the mugration bug
-* [```c47e340```](https://github.com/ktmeaton/plague-phylogeography/commit/c47e340) morelli nextstrain config and metadata
-* [```c711b5b```](https://github.com/ktmeaton/plague-phylogeography/commit/c711b5b) exhibit doc up to auspice server
-* [```4f056f5```](https://github.com/ktmeaton/plague-phylogeography/commit/4f056f5) update metadata formatting
-* [```a73d376```](https://github.com/ktmeaton/plague-phylogeography/commit/a73d376) rename example exec
-* [```0f3fccb```](https://github.com/ktmeaton/plague-phylogeography/commit/0f3fccb) remove iqtree branch supports that conflict with nextstrain
-* [```8a09dee```](https://github.com/ktmeaton/plague-phylogeography/commit/8a09dee) morelli annotations
-* [```f947e76```](https://github.com/ktmeaton/plague-phylogeography/commit/f947e76) remove debug command
-* [```aaa24ee```](https://github.com/ktmeaton/plague-phylogeography/commit/aaa24ee) add exhibit docs
-* [```e1fee69```](https://github.com/ktmeaton/plague-phylogeography/commit/e1fee69) remove bad v1 assembly links
-* [```19f8dd5```](https://github.com/ktmeaton/plague-phylogeography/commit/19f8dd5) manually fix morelli ftp link
-* [```9003019```](https://github.com/ktmeaton/plague-phylogeography/commit/9003019) more convoluted if to skip sra
-* [```65523ed```](https://github.com/ktmeaton/plague-phylogeography/commit/65523ed) add morelli annotations
-* [```d3082a6```](https://github.com/ktmeaton/plague-phylogeography/commit/d3082a6) note about graphviz
-* [```d70398f```](https://github.com/ktmeaton/plague-phylogeography/commit/d70398f) pipeline update for sra script
-* [```58a4333```](https://github.com/ktmeaton/plague-phylogeography/commit/58a4333) script fix for sqlite EAGER
-* [```72b7b12```](https://github.com/ktmeaton/plague-phylogeography/commit/72b7b12) remove ftp links an dbug fix
-* [```87ba466```](https://github.com/ktmeaton/plague-phylogeography/commit/87ba466) before removing ftp url
-* [```064e1d3```](https://github.com/ktmeaton/plague-phylogeography/commit/064e1d3) limit EAGER to 4 samples
-* [```985e621```](https://github.com/ktmeaton/plague-phylogeography/commit/985e621) skip bam files
-* [```2d2adff```](https://github.com/ktmeaton/plague-phylogeography/commit/2d2adff) sra acc bugfix
-* [```aa0f932```](https://github.com/ktmeaton/plague-phylogeography/commit/aa0f932) linting
-* [```7f01ae2```](https://github.com/ktmeaton/plague-phylogeography/commit/7f01ae2) add the sra tools for download
-* [```c734ed2```](https://github.com/ktmeaton/plague-phylogeography/commit/c734ed2) allow 2 ancient eager samples
-* [```5aece99```](https://github.com/ktmeaton/plague-phylogeography/commit/5aece99) important bug fix for multi record
-* [```0e7ae90```](https://github.com/ktmeaton/plague-phylogeography/commit/0e7ae90) prototype sra download process
-* [```bf10d7b```](https://github.com/ktmeaton/plague-phylogeography/commit/bf10d7b) db update to specify EAGER records
-* [```e001d7f```](https://github.com/ktmeaton/plague-phylogeography/commit/e001d7f) basic eager process start
-* [```49aa056```](https://github.com/ktmeaton/plague-phylogeography/commit/49aa056) eager instructions
-* [```9364885```](https://github.com/ktmeaton/plague-phylogeography/commit/9364885) line continue typo
-* [```b72ffb2```](https://github.com/ktmeaton/plague-phylogeography/commit/b72ffb2) try to rename process
-* [```87d0855```](https://github.com/ktmeaton/plague-phylogeography/commit/87d0855) remove outdated annotation
-* [```60fd6dc```](https://github.com/ktmeaton/plague-phylogeography/commit/60fd6dc) remove outdated annotation
+* [```1c5e86af```](https://github.com/ktmeaton/plague-phylogeography/commit/1c5e86af) update to v0.1.3
+* [```012f4917```](https://github.com/ktmeaton/plague-phylogeography/commit/012f4917) fix typos
+* [```240cd82b```](https://github.com/ktmeaton/plague-phylogeography/commit/240cd82b) fix tree compare link
+* [```c1b059bc```](https://github.com/ktmeaton/plague-phylogeography/commit/c1b059bc) fix tree compare link
+* [```8b15cfe4```](https://github.com/ktmeaton/plague-phylogeography/commit/8b15cfe4) recording draft
+* [```96b161b4```](https://github.com/ktmeaton/plague-phylogeography/commit/96b161b4) update links
+* [```da9ca425```](https://github.com/ktmeaton/plague-phylogeography/commit/da9ca425) clean up status
+* [```6157e45f```](https://github.com/ktmeaton/plague-phylogeography/commit/6157e45f) ready for proofreading
+* [```bf11a24e```](https://github.com/ktmeaton/plague-phylogeography/commit/bf11a24e) up to interdisc
+* [```52261202```](https://github.com/ktmeaton/plague-phylogeography/commit/52261202) begin editing
+* [```3f7864a9```](https://github.com/ktmeaton/plague-phylogeography/commit/3f7864a9) remove test hrule
+* [```2f02c64e```](https://github.com/ktmeaton/plague-phylogeography/commit/2f02c64e) test hrule
+* [```676c1082```](https://github.com/ktmeaton/plague-phylogeography/commit/676c1082) first page color country
+* [```baf1ea0d```](https://github.com/ktmeaton/plague-phylogeography/commit/baf1ea0d) first page color country
+* [```aa32d334```](https://github.com/ktmeaton/plague-phylogeography/commit/aa32d334) draft up to publish
+* [```0af4add5```](https://github.com/ktmeaton/plague-phylogeography/commit/0af4add5) draft of playground
+* [```ef88220b```](https://github.com/ktmeaton/plague-phylogeography/commit/ef88220b) first two pages initial
+* [```03c8635c```](https://github.com/ktmeaton/plague-phylogeography/commit/03c8635c) fix single dataset
+* [```1ab3648b```](https://github.com/ktmeaton/plague-phylogeography/commit/1ab3648b) upload DHSI narrative
+* [```e23a79e4```](https://github.com/ktmeaton/plague-phylogeography/commit/e23a79e4) update cui2013 with new uncertainty param
+* [```ff0102d3```](https://github.com/ktmeaton/plague-phylogeography/commit/ff0102d3) date range temp fix
+* [```7507f3c7```](https://github.com/ktmeaton/plague-phylogeography/commit/7507f3c7) add nexus newick script
+* [```2761f9ee```](https://github.com/ktmeaton/plague-phylogeography/commit/2761f9ee) save before changing date format
+* [```ffd79c72```](https://github.com/ktmeaton/plague-phylogeography/commit/ffd79c72) new augur param for morelli
+* [```84d07ce9```](https://github.com/ktmeaton/plague-phylogeography/commit/84d07ce9) update morelli json
+* [```0c716644```](https://github.com/ktmeaton/plague-phylogeography/commit/0c716644) change date coloring and move files
+* [```e0c8c97d```](https://github.com/ktmeaton/plague-phylogeography/commit/e0c8c97d) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```03b5f057```](https://github.com/ktmeaton/plague-phylogeography/commit/03b5f057) remove Angola json auspice
+* [```d325bca2```](https://github.com/ktmeaton/plague-phylogeography/commit/d325bca2) simplify metadata section
+* [```fac540a5```](https://github.com/ktmeaton/plague-phylogeography/commit/fac540a5) put wildcard output first
+* [```819f2345```](https://github.com/ktmeaton/plague-phylogeography/commit/819f2345) fix snippy multi resume bug
+* [```adcf3937```](https://github.com/ktmeaton/plague-phylogeography/commit/adcf3937) note about fail to publish issue
+* [```b92fd6be```](https://github.com/ktmeaton/plague-phylogeography/commit/b92fd6be) REMOVE Angola strain
+* [```1fd8a68b```](https://github.com/ktmeaton/plague-phylogeography/commit/1fd8a68b) docs before disabling covariance
+* [```d98c0464```](https://github.com/ktmeaton/plague-phylogeography/commit/d98c0464) strain date interval
+* [```3d510942```](https://github.com/ktmeaton/plague-phylogeography/commit/3d510942) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```49f1855d```](https://github.com/ktmeaton/plague-phylogeography/commit/49f1855d) add cui 2013 treefile
+* [```ba70cd3f```](https://github.com/ktmeaton/plague-phylogeography/commit/ba70cd3f) export auspice copy command
+* [```3e0093a9```](https://github.com/ktmeaton/plague-phylogeography/commit/3e0093a9) add cui 2013 auspice files
+* [```4763fadd```](https://github.com/ktmeaton/plague-phylogeography/commit/4763fadd) add cui2013 auspice config
+* [```065e1c8f```](https://github.com/ktmeaton/plague-phylogeography/commit/065e1c8f) remove old unused auspice datasets
+* [```86902817```](https://github.com/ktmeaton/plague-phylogeography/commit/86902817) add auspice morelli
+* [```9652e128```](https://github.com/ktmeaton/plague-phylogeography/commit/9652e128) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```a52670ff```](https://github.com/ktmeaton/plague-phylogeography/commit/a52670ff) more labels for colorings
+* [```538ac318```](https://github.com/ktmeaton/plague-phylogeography/commit/538ac318) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```0e7c4a60```](https://github.com/ktmeaton/plague-phylogeography/commit/0e7c4a60) morelli updates
+* [```f7964bf3```](https://github.com/ktmeaton/plague-phylogeography/commit/f7964bf3) update auspice config morelli
+* [```f9280646```](https://github.com/ktmeaton/plague-phylogeography/commit/f9280646) standardize biovar med spelling
+* [```af0d9e5a```](https://github.com/ktmeaton/plague-phylogeography/commit/af0d9e5a) metadata prep complete
+* [```f4cfd1f3```](https://github.com/ktmeaton/plague-phylogeography/commit/f4cfd1f3) major cui annot and docs
+* [```b52db233```](https://github.com/ktmeaton/plague-phylogeography/commit/b52db233) begin adding cui docs
+* [```5f060ff7```](https://github.com/ktmeaton/plague-phylogeography/commit/5f060ff7) update cui and morelli host info
+* [```51f58e38```](https://github.com/ktmeaton/plague-phylogeography/commit/51f58e38) update before cui2013 run
+* [```d765bf51```](https://github.com/ktmeaton/plague-phylogeography/commit/d765bf51) augur trees and plots
+* [```0a32f38c```](https://github.com/ktmeaton/plague-phylogeography/commit/0a32f38c) notes on treetime vs augur refine
+* [```d778addf```](https://github.com/ktmeaton/plague-phylogeography/commit/d778addf) fixed the mugration bug
+* [```c47e340a```](https://github.com/ktmeaton/plague-phylogeography/commit/c47e340a) morelli nextstrain config and metadata
+* [```c711b5b4```](https://github.com/ktmeaton/plague-phylogeography/commit/c711b5b4) exhibit doc up to auspice server
+* [```4f056f5a```](https://github.com/ktmeaton/plague-phylogeography/commit/4f056f5a) update metadata formatting
+* [```a73d376c```](https://github.com/ktmeaton/plague-phylogeography/commit/a73d376c) rename example exec
+* [```0f3fccbc```](https://github.com/ktmeaton/plague-phylogeography/commit/0f3fccbc) remove iqtree branch supports that conflict with nextstrain
+* [```8a09deea```](https://github.com/ktmeaton/plague-phylogeography/commit/8a09deea) morelli annotations
+* [```f947e766```](https://github.com/ktmeaton/plague-phylogeography/commit/f947e766) remove debug command
+* [```aaa24ee3```](https://github.com/ktmeaton/plague-phylogeography/commit/aaa24ee3) add exhibit docs
+* [```e1fee69a```](https://github.com/ktmeaton/plague-phylogeography/commit/e1fee69a) remove bad v1 assembly links
+* [```19f8dd56```](https://github.com/ktmeaton/plague-phylogeography/commit/19f8dd56) manually fix morelli ftp link
+* [```90030199```](https://github.com/ktmeaton/plague-phylogeography/commit/90030199) more convoluted if to skip sra
+* [```65523ed6```](https://github.com/ktmeaton/plague-phylogeography/commit/65523ed6) add morelli annotations
+* [```d3082a68```](https://github.com/ktmeaton/plague-phylogeography/commit/d3082a68) note about graphviz
+* [```d70398f3```](https://github.com/ktmeaton/plague-phylogeography/commit/d70398f3) pipeline update for sra script
+* [```58a43333```](https://github.com/ktmeaton/plague-phylogeography/commit/58a43333) script fix for sqlite EAGER
+* [```72b7b122```](https://github.com/ktmeaton/plague-phylogeography/commit/72b7b122) remove ftp links an dbug fix
+* [```87ba4668```](https://github.com/ktmeaton/plague-phylogeography/commit/87ba4668) before removing ftp url
+* [```064e1d32```](https://github.com/ktmeaton/plague-phylogeography/commit/064e1d32) limit EAGER to 4 samples
+* [```985e621b```](https://github.com/ktmeaton/plague-phylogeography/commit/985e621b) skip bam files
+* [```2d2adffd```](https://github.com/ktmeaton/plague-phylogeography/commit/2d2adffd) sra acc bugfix
+* [```aa0f9321```](https://github.com/ktmeaton/plague-phylogeography/commit/aa0f9321) linting
+* [```7f01ae25```](https://github.com/ktmeaton/plague-phylogeography/commit/7f01ae25) add the sra tools for download
+* [```c734ed2d```](https://github.com/ktmeaton/plague-phylogeography/commit/c734ed2d) allow 2 ancient eager samples
+* [```5aece994```](https://github.com/ktmeaton/plague-phylogeography/commit/5aece994) important bug fix for multi record
+* [```0e7ae90a```](https://github.com/ktmeaton/plague-phylogeography/commit/0e7ae90a) prototype sra download process
+* [```bf10d7bc```](https://github.com/ktmeaton/plague-phylogeography/commit/bf10d7bc) db update to specify EAGER records
+* [```e001d7fc```](https://github.com/ktmeaton/plague-phylogeography/commit/e001d7fc) basic eager process start
+* [```49aa0569```](https://github.com/ktmeaton/plague-phylogeography/commit/49aa0569) eager instructions
+* [```93648857```](https://github.com/ktmeaton/plague-phylogeography/commit/93648857) line continue typo
+* [```b72ffb2c```](https://github.com/ktmeaton/plague-phylogeography/commit/b72ffb2c) try to rename process
+* [```87d0855b```](https://github.com/ktmeaton/plague-phylogeography/commit/87d0855b) remove outdated annotation
+* [```60fd6dcb```](https://github.com/ktmeaton/plague-phylogeography/commit/60fd6dcb) remove outdated annotation
 
 ## v0.1.2
 
 ### Commits
 
-* [```2e2042f```](https://github.com/ktmeaton/plague-phylogeography/commit/2e2042f) final tidy before release
-* [```b744835```](https://github.com/ktmeaton/plague-phylogeography/commit/b744835) run workflows on published release
-* [```49660c4```](https://github.com/ktmeaton/plague-phylogeography/commit/49660c4) future note python linting
-* [```ba58eeb```](https://github.com/ktmeaton/plague-phylogeography/commit/ba58eeb) split max_datasets into 2 param
-* [```ee1eff8```](https://github.com/ktmeaton/plague-phylogeography/commit/ee1eff8) correct iqtree threads param
-* [```973a33d```](https://github.com/ktmeaton/plague-phylogeography/commit/973a33d) try setting iqtree cores to AUTO
-* [```6bd4861```](https://github.com/ktmeaton/plague-phylogeography/commit/6bd4861) update iqtree to version 2
-* [```39563c3```](https://github.com/ktmeaton/plague-phylogeography/commit/39563c3) snippy use snpeff with ref genome data dir
-* [```887e806```](https://github.com/ktmeaton/plague-phylogeography/commit/887e806) update db building
-* [```2bc3124```](https://github.com/ktmeaton/plague-phylogeography/commit/2bc3124) specify docs path
-* [```915f8e7```](https://github.com/ktmeaton/plague-phylogeography/commit/915f8e7) fix snpeff process heading
-* [```4872aff```](https://github.com/ktmeaton/plague-phylogeography/commit/4872aff) force python 3.7
-* [```216aadc```](https://github.com/ktmeaton/plague-phylogeography/commit/216aadc) test sphinx build install
-* [```f3bc2d9```](https://github.com/ktmeaton/plague-phylogeography/commit/f3bc2d9) make snpeff database local
-* [```2189942```](https://github.com/ktmeaton/plague-phylogeography/commit/2189942) add a sphinx docs workflow
-* [```5fdc407```](https://github.com/ktmeaton/plague-phylogeography/commit/5fdc407) add base sphinx to dev env
-* [```f167277```](https://github.com/ktmeaton/plague-phylogeography/commit/f167277) make snpeff path system generic
-* [```b72465e```](https://github.com/ktmeaton/plague-phylogeography/commit/b72465e) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```4e31a41```](https://github.com/ktmeaton/plague-phylogeography/commit/4e31a41) snpeff db build
-* [```af6958f```](https://github.com/ktmeaton/plague-phylogeography/commit/af6958f) snpeff and gb process doc update
-* [```5b7d08a```](https://github.com/ktmeaton/plague-phylogeography/commit/5b7d08a) comment out unnecessary db param
-* [```3c2625d```](https://github.com/ktmeaton/plague-phylogeography/commit/3c2625d) add new artifacts
-* [```5619c3c```](https://github.com/ktmeaton/plague-phylogeography/commit/5619c3c) remove rst lint
-* [```fb829fe```](https://github.com/ktmeaton/plague-phylogeography/commit/fb829fe) locally confirmed pipeline
-* [```547d33c```](https://github.com/ktmeaton/plague-phylogeography/commit/547d33c) disable rst linting
-* [```387cce8```](https://github.com/ktmeaton/plague-phylogeography/commit/387cce8) lint and actions update
-* [```020aebf```](https://github.com/ktmeaton/plague-phylogeography/commit/020aebf) switch snippy pairwise to gb ref
-* [```8610d38```](https://github.com/ktmeaton/plague-phylogeography/commit/8610d38) remove geopy from env
-* [```3dd5861```](https://github.com/ktmeaton/plague-phylogeography/commit/3dd5861) finish draft snpeff build db
-* [```8c78bb7```](https://github.com/ktmeaton/plague-phylogeography/commit/8c78bb7) began work on snpeff build db
-* [```e65a705```](https://github.com/ktmeaton/plague-phylogeography/commit/e65a705) remove rule exception
-* [```3957d6a```](https://github.com/ktmeaton/plague-phylogeography/commit/3957d6a) change sql queries to KEEP and EAGER
-* [```2985119```](https://github.com/ktmeaton/plague-phylogeography/commit/2985119) heading spacing
-* [```e267be0```](https://github.com/ktmeaton/plague-phylogeography/commit/e267be0) rst-lint desc
-* [```df9daee```](https://github.com/ktmeaton/plague-phylogeography/commit/df9daee) rst-lint desc
-* [```632cba2```](https://github.com/ktmeaton/plague-phylogeography/commit/632cba2) ignore md line length rule
-* [```a758dda```](https://github.com/ktmeaton/plague-phylogeography/commit/a758dda) ignore md line length rule
-* [```27a3a6b```](https://github.com/ktmeaton/plague-phylogeography/commit/27a3a6b) add geopy to environment
-* [```1a44666```](https://github.com/ktmeaton/plague-phylogeography/commit/1a44666) database update with new text export
-* [```d05ed71```](https://github.com/ktmeaton/plague-phylogeography/commit/d05ed71) force string conversion of values
-* [```4583752```](https://github.com/ktmeaton/plague-phylogeography/commit/4583752) simplify rst lint description
-* [```2d9255b```](https://github.com/ktmeaton/plague-phylogeography/commit/2d9255b) add rst linting to workflow
-* [```9d6b20b```](https://github.com/ktmeaton/plague-phylogeography/commit/9d6b20b) add rst linter
-* [```a86c6dc```](https://github.com/ktmeaton/plague-phylogeography/commit/a86c6dc) update ncbimeta_annotate docs
-* [```55dbb8d```](https://github.com/ktmeaton/plague-phylogeography/commit/55dbb8d) add export to ncbimeta_update
-* [```421639c```](https://github.com/ktmeaton/plague-phylogeography/commit/421639c) add markdownlint pre-commit
-* [```39d1723```](https://github.com/ktmeaton/plague-phylogeography/commit/39d1723) fully commented biosample
-* [```9f0d93a```](https://github.com/ktmeaton/plague-phylogeography/commit/9f0d93a) start the KEEP annotations
-* [```738582a```](https://github.com/ktmeaton/plague-phylogeography/commit/738582a) finish peru annotations
-* [```fab10f3```](https://github.com/ktmeaton/plague-phylogeography/commit/fab10f3) finish cui annotations
-* [```3902168```](https://github.com/ktmeaton/plague-phylogeography/commit/3902168) start EAGER annot and lab
-* [```ffe6bff```](https://github.com/ktmeaton/plague-phylogeography/commit/ffe6bff) add not yp comments
-* [```176ca2e```](https://github.com/ktmeaton/plague-phylogeography/commit/176ca2e) minor edit to run
-* [```0ced3ac```](https://github.com/ktmeaton/plague-phylogeography/commit/0ced3ac) add excutable permissions to scripts
-* [```5816897```](https://github.com/ktmeaton/plague-phylogeography/commit/5816897) any lint files
-* [```004c141```](https://github.com/ktmeaton/plague-phylogeography/commit/004c141) fix indentation
-* [```8e0010f```](https://github.com/ktmeaton/plague-phylogeography/commit/8e0010f) remove problematic name key
-* [```7a37b47```](https://github.com/ktmeaton/plague-phylogeography/commit/7a37b47) place pipeline in conda env
-* [```e4e92e6```](https://github.com/ktmeaton/plague-phylogeography/commit/e4e92e6) disable ordered list lint
-* [```5c6b1be```](https://github.com/ktmeaton/plague-phylogeography/commit/5c6b1be) use gh actions for conda setup
-* [```2e49286```](https://github.com/ktmeaton/plague-phylogeography/commit/2e49286) add ordered list linting
-* [```5f45729```](https://github.com/ktmeaton/plague-phylogeography/commit/5f45729) fix mixed line endings
-* [```bb534fc```](https://github.com/ktmeaton/plague-phylogeography/commit/bb534fc) add pipeline workflow
-* [```039463c```](https://github.com/ktmeaton/plague-phylogeography/commit/039463c) README linting
-* [```5329431```](https://github.com/ktmeaton/plague-phylogeography/commit/5329431) try restrict lint
-* [```d855191```](https://github.com/ktmeaton/plague-phylogeography/commit/d855191) language for fenced code block
-* [```4a2de62```](https://github.com/ktmeaton/plague-phylogeography/commit/4a2de62) lint format blanks around headings and lists
-* [```885b1d7```](https://github.com/ktmeaton/plague-phylogeography/commit/885b1d7) add markdown linting action
-* [```3bd64fe```](https://github.com/ktmeaton/plague-phylogeography/commit/3bd64fe) relocate nextstrain metadata
-* [```10380a8```](https://github.com/ktmeaton/plague-phylogeography/commit/10380a8) improved dev env instructions
-* [```c6136af```](https://github.com/ktmeaton/plague-phylogeography/commit/c6136af) dev dependencies and pre-commit
-* [```4d52972```](https://github.com/ktmeaton/plague-phylogeography/commit/4d52972) remove after rename
-* [```c9b44e4```](https://github.com/ktmeaton/plague-phylogeography/commit/c9b44e4) rename extension
-* [```7c884c9```](https://github.com/ktmeaton/plague-phylogeography/commit/7c884c9) update ncbimeta to remove annot file
-* [```282e4f4```](https://github.com/ktmeaton/plague-phylogeography/commit/282e4f4) annot remove long branch sample
-* [```5b1a8a1```](https://github.com/ktmeaton/plague-phylogeography/commit/5b1a8a1) remove the test pipeline
-* [```dc2f62a```](https://github.com/ktmeaton/plague-phylogeography/commit/dc2f62a) add the sed replacement
-* [```d05e19a```](https://github.com/ktmeaton/plague-phylogeography/commit/d05e19a) switch to new annotation format
-* [```102d800```](https://github.com/ktmeaton/plague-phylogeography/commit/102d800) include no data char as parameter
-* [```dd2e6c1```](https://github.com/ktmeaton/plague-phylogeography/commit/dd2e6c1) deal with unescaped quotes in annotation
-* [```caefeb4```](https://github.com/ktmeaton/plague-phylogeography/commit/caefeb4) more convoluted if skipping
-* [```2bc5ad3```](https://github.com/ktmeaton/plague-phylogeography/commit/2bc5ad3) incorporate ncbimeta annot if
-* [```5200f86```](https://github.com/ktmeaton/plague-phylogeography/commit/5200f86) db annot update skipping
-* [```9f83f0e```](https://github.com/ktmeaton/plague-phylogeography/commit/9f83f0e) misc metadata
-* [```ecb2cea```](https://github.com/ktmeaton/plague-phylogeography/commit/ecb2cea) allowing skipping
-* [```eb3223d```](https://github.com/ktmeaton/plague-phylogeography/commit/eb3223d) test conditional input with filename
-* [```99f8ffa```](https://github.com/ktmeaton/plague-phylogeography/commit/99f8ffa) additional skip variables
-* [```6d8c592```](https://github.com/ktmeaton/plague-phylogeography/commit/6d8c592) convoluted if statements to allow skipping
-* [```91c168d```](https://github.com/ktmeaton/plague-phylogeography/commit/91c168d) don't try to geocode values like missing or unknown
-* [```1c8210b```](https://github.com/ktmeaton/plague-phylogeography/commit/1c8210b) first draft at geocode script
-* [```b5e65a9```](https://github.com/ktmeaton/plague-phylogeography/commit/b5e65a9) commit before simplify try block
-* [```2b6484d```](https://github.com/ktmeaton/plague-phylogeography/commit/2b6484d) executable geocode script
-* [```a6aa218```](https://github.com/ktmeaton/plague-phylogeography/commit/a6aa218) script to automate geocoding
-* [```b54ffbd```](https://github.com/ktmeaton/plague-phylogeography/commit/b54ffbd) geocoding notes
-* [```26b2bb2```](https://github.com/ktmeaton/plague-phylogeography/commit/26b2bb2) more nextstrain edits
-* [```c1d776e```](https://github.com/ktmeaton/plague-phylogeography/commit/c1d776e) demo metadata files for annot and nextstrain
-* [```ac954d0```](https://github.com/ktmeaton/plague-phylogeography/commit/ac954d0) nextstrain metadata task
-* [```f976c92```](https://github.com/ktmeaton/plague-phylogeography/commit/f976c92) remove split col processing
-* [```6defb80```](https://github.com/ktmeaton/plague-phylogeography/commit/6defb80) last commit before give up split col
-* [```0ad7164```](https://github.com/ktmeaton/plague-phylogeography/commit/0ad7164) better db checking
-* [```9ceeef2```](https://github.com/ktmeaton/plague-phylogeography/commit/9ceeef2) better db file checking
-* [```22e5fb5```](https://github.com/ktmeaton/plague-phylogeography/commit/22e5fb5) nextstrain convert to tsv
-* [```c4664da```](https://github.com/ktmeaton/plague-phylogeography/commit/c4664da) v0.1.2 init changes
-* [```a2f6e9e```](https://github.com/ktmeaton/plague-phylogeography/commit/a2f6e9e) proper project name filtering for bronze age
-* [```2d7185e```](https://github.com/ktmeaton/plague-phylogeography/commit/2d7185e) space format
-* [```c036106```](https://github.com/ktmeaton/plague-phylogeography/commit/c036106) notes on annot db prep
-* [```8ab4472```](https://github.com/ktmeaton/plague-phylogeography/commit/8ab4472) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
-* [```1ed03ce```](https://github.com/ktmeaton/plague-phylogeography/commit/1ed03ce) multiqc cross-ref and channels
-* [```8f12195```](https://github.com/ktmeaton/plague-phylogeography/commit/8f12195) qualimap cross-ref and channels
-* [```234204a```](https://github.com/ktmeaton/plague-phylogeography/commit/234204a) qualimap cross-ref and channels
-* [```ad7b0d9```](https://github.com/ktmeaton/plague-phylogeography/commit/ad7b0d9) include phylogeny and nextstrain pages
-* [```a058ffa```](https://github.com/ktmeaton/plague-phylogeography/commit/a058ffa) create new phylogeny and nextstrain pages
-* [```272edac```](https://github.com/ktmeaton/plague-phylogeography/commit/272edac) iqtree cross-ref and channels
-* [```1643771```](https://github.com/ktmeaton/plague-phylogeography/commit/1643771) snippy multi filter
-* [```2ca3eff```](https://github.com/ktmeaton/plague-phylogeography/commit/2ca3eff) fix bad links snippy docs
-* [```982bf8d```](https://github.com/ktmeaton/plague-phylogeography/commit/982bf8d) fix bad links
-* [```e639197```](https://github.com/ktmeaton/plague-phylogeography/commit/e639197) added snippy multi process doc
-* [```5597f55```](https://github.com/ktmeaton/plague-phylogeography/commit/5597f55) merge mask bed cross-ref and channels
-* [```ffd16aa```](https://github.com/ktmeaton/plague-phylogeography/commit/ffd16aa) snp density cross-ref and channels
-* [```a18c4f1```](https://github.com/ktmeaton/plague-phylogeography/commit/a18c4f1) remove unnecessary variant summary process
-* [```77dd6b7```](https://github.com/ktmeaton/plague-phylogeography/commit/77dd6b7) commit before variant summary collect rewrite
-* [```e2adfdf```](https://github.com/ktmeaton/plague-phylogeography/commit/e2adfdf) variant summary ch and cross-ref
-* [```5db4635```](https://github.com/ktmeaton/plague-phylogeography/commit/5db4635) add bam to pairwise snippy doc publish
-* [```d05278b```](https://github.com/ktmeaton/plague-phylogeography/commit/d05278b) pairwise snippy cross-ref, channels, script
-* [```5a826c2```](https://github.com/ktmeaton/plague-phylogeography/commit/5a826c2) New KEEP to BioSample and Master
-* [```a0b7700```](https://github.com/ktmeaton/plague-phylogeography/commit/a0b7700) low complexity cross-ref and channel
-* [```fd7dc07```](https://github.com/ktmeaton/plague-phylogeography/commit/fd7dc07) detect repeats cross-ref and publish update
-* [```4e1ecc2```](https://github.com/ktmeaton/plague-phylogeography/commit/4e1ecc2) update shell script and cross-ref
-* [```543e01a```](https://github.com/ktmeaton/plague-phylogeography/commit/543e01a) make ref fasta editing generic to match gb
-* [```beb569c```](https://github.com/ktmeaton/plague-phylogeography/commit/beb569c) note automate snpeff tbd
-* [```face726```](https://github.com/ktmeaton/plague-phylogeography/commit/face726) update assembly cross-ref
-* [```d1567af```](https://github.com/ktmeaton/plague-phylogeography/commit/d1567af) update descriptions and channels
-* [```d713d24```](https://github.com/ktmeaton/plague-phylogeography/commit/d713d24) eager params and new sqlite query
-* [```f82390f```](https://github.com/ktmeaton/plague-phylogeography/commit/f82390f) use script to prep SRA metadata for EAGER tsv
-* [```58eaf5b```](https://github.com/ktmeaton/plague-phylogeography/commit/58eaf5b) allow --max-datasets as parameter
-* [```658a58f```](https://github.com/ktmeaton/plague-phylogeography/commit/658a58f) update description and help commands
-* [```56584fc```](https://github.com/ktmeaton/plague-phylogeography/commit/56584fc) script to prep EAGER tsv input from sqlite
-* [```1a5a6b3```](https://github.com/ktmeaton/plague-phylogeography/commit/1a5a6b3) update docs and add process cross-ref
-* [```55e0792```](https://github.com/ktmeaton/plague-phylogeography/commit/55e0792) add sphinx extension for cross ref
-* [```ea86c37```](https://github.com/ktmeaton/plague-phylogeography/commit/ea86c37) remove h1 header from title
-* [```b48fc31```](https://github.com/ktmeaton/plague-phylogeography/commit/b48fc31) fix ref 8
-* [```cd2f266```](https://github.com/ktmeaton/plague-phylogeography/commit/cd2f266) reference rearrange (1-11)
-* [```9a17930```](https://github.com/ktmeaton/plague-phylogeography/commit/9a17930) heading size in abstract
-* [```90f835f```](https://github.com/ktmeaton/plague-phylogeography/commit/90f835f) title simplify more
-* [```6821caf```](https://github.com/ktmeaton/plague-phylogeography/commit/6821caf) explain Swedish finding significance
-* [```e0b2cf8```](https://github.com/ktmeaton/plague-phylogeography/commit/e0b2cf8) modern dna to ancient transition
-* [```57f46cf```](https://github.com/ktmeaton/plague-phylogeography/commit/57f46cf) fix restart animation link
-* [```6724884```](https://github.com/ktmeaton/plague-phylogeography/commit/6724884) origins dna update
-* [```ed052b4```](https://github.com/ktmeaton/plague-phylogeography/commit/ed052b4) simplified titles
-* [```234de86```](https://github.com/ktmeaton/plague-phylogeography/commit/234de86) minor grammar
-* [```8454057```](https://github.com/ktmeaton/plague-phylogeography/commit/8454057) remove iconic maps section
-* [```a022e2f```](https://github.com/ktmeaton/plague-phylogeography/commit/a022e2f) explain reconstruction
-* [```2b1cf70```](https://github.com/ktmeaton/plague-phylogeography/commit/2b1cf70) rearrange
-* [```adac8af```](https://github.com/ktmeaton/plague-phylogeography/commit/adac8af) origins edits
-* [```436bad0```](https://github.com/ktmeaton/plague-phylogeography/commit/436bad0) center justify left side text links
-* [```ed31b70```](https://github.com/ktmeaton/plague-phylogeography/commit/ed31b70) remove test commands (SUCCESS)
-* [```3264277```](https://github.com/ktmeaton/plague-phylogeography/commit/3264277) test remote change with heading
-* [```a9bf5f0```](https://github.com/ktmeaton/plague-phylogeography/commit/a9bf5f0) try p tag outside of abstract
-* [```b5e2da1```](https://github.com/ktmeaton/plague-phylogeography/commit/b5e2da1) CSS remote test 2
-* [```f1a8531```](https://github.com/ktmeaton/plague-phylogeography/commit/f1a8531) CSS Override Remote?
-* [```1607405```](https://github.com/ktmeaton/plague-phylogeography/commit/1607405) CSS Override
-* [```2b11baf```](https://github.com/ktmeaton/plague-phylogeography/commit/2b11baf) remove the DemoMap test
-* [```2a50b97```](https://github.com/ktmeaton/plague-phylogeography/commit/2a50b97) correct heading size
-* [```96e13ca```](https://github.com/ktmeaton/plague-phylogeography/commit/96e13ca) github actions reminder
-* [```37e452d```](https://github.com/ktmeaton/plague-phylogeography/commit/37e452d) switch all bold md to html tags
-* [```61af328```](https://github.com/ktmeaton/plague-phylogeography/commit/61af328) accept cmd line args
-* [```8862bb8```](https://github.com/ktmeaton/plague-phylogeography/commit/8862bb8) test html bold tag
-* [```f560319```](https://github.com/ktmeaton/plague-phylogeography/commit/f560319) writing edits and autogen
-* [```79c048c```](https://github.com/ktmeaton/plague-phylogeography/commit/79c048c) script to convert local to remote
-* [```431d830```](https://github.com/ktmeaton/plague-phylogeography/commit/431d830) bolding and tidying
-* [```2d07feb```](https://github.com/ktmeaton/plague-phylogeography/commit/2d07feb) all bib items updated
-* [```259e44b```](https://github.com/ktmeaton/plague-phylogeography/commit/259e44b) bib up to origins ancient dna
-* [```ba9311b```](https://github.com/ktmeaton/plague-phylogeography/commit/ba9311b) bib up to origins history
-* [```0bd7c80```](https://github.com/ktmeaton/plague-phylogeography/commit/0bd7c80) started footnote style
-* [```924d49b```](https://github.com/ktmeaton/plague-phylogeography/commit/924d49b) switch to superscript reference
-* [```194c8cc```](https://github.com/ktmeaton/plague-phylogeography/commit/194c8cc) add local specifier
-* [```040b914```](https://github.com/ktmeaton/plague-phylogeography/commit/040b914) breka up long sentence
-* [```e2b205a```](https://github.com/ktmeaton/plague-phylogeography/commit/e2b205a) wording area vs lineages
-* [```83c91be```](https://github.com/ktmeaton/plague-phylogeography/commit/83c91be) rename to repo prefix
-* [```d9ca101```](https://github.com/ktmeaton/plague-phylogeography/commit/d9ca101) plague SCDS 2020 remote narrative
-* [```f9bb407```](https://github.com/ktmeaton/plague-phylogeography/commit/f9bb407) before remote switch
-* [```9158897```](https://github.com/ktmeaton/plague-phylogeography/commit/9158897) add table of contents
+* [```2e2042f2```](https://github.com/ktmeaton/plague-phylogeography/commit/2e2042f2) final tidy before release
+* [```b7448353```](https://github.com/ktmeaton/plague-phylogeography/commit/b7448353) run workflows on published release
+* [```49660c49```](https://github.com/ktmeaton/plague-phylogeography/commit/49660c49) future note python linting
+* [```ba58eebb```](https://github.com/ktmeaton/plague-phylogeography/commit/ba58eebb) split max_datasets into 2 param
+* [```ee1eff8e```](https://github.com/ktmeaton/plague-phylogeography/commit/ee1eff8e) correct iqtree threads param
+* [```973a33d0```](https://github.com/ktmeaton/plague-phylogeography/commit/973a33d0) try setting iqtree cores to AUTO
+* [```6bd48615```](https://github.com/ktmeaton/plague-phylogeography/commit/6bd48615) update iqtree to version 2
+* [```39563c3e```](https://github.com/ktmeaton/plague-phylogeography/commit/39563c3e) snippy use snpeff with ref genome data dir
+* [```887e8061```](https://github.com/ktmeaton/plague-phylogeography/commit/887e8061) update db building
+* [```2bc31244```](https://github.com/ktmeaton/plague-phylogeography/commit/2bc31244) specify docs path
+* [```915f8e77```](https://github.com/ktmeaton/plague-phylogeography/commit/915f8e77) fix snpeff process heading
+* [```4872aff1```](https://github.com/ktmeaton/plague-phylogeography/commit/4872aff1) force python 3.7
+* [```216aadc0```](https://github.com/ktmeaton/plague-phylogeography/commit/216aadc0) test sphinx build install
+* [```f3bc2d9c```](https://github.com/ktmeaton/plague-phylogeography/commit/f3bc2d9c) make snpeff database local
+* [```2189942c```](https://github.com/ktmeaton/plague-phylogeography/commit/2189942c) add a sphinx docs workflow
+* [```5fdc4079```](https://github.com/ktmeaton/plague-phylogeography/commit/5fdc4079) add base sphinx to dev env
+* [```f1672774```](https://github.com/ktmeaton/plague-phylogeography/commit/f1672774) make snpeff path system generic
+* [```b72465e5```](https://github.com/ktmeaton/plague-phylogeography/commit/b72465e5) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```4e31a412```](https://github.com/ktmeaton/plague-phylogeography/commit/4e31a412) snpeff db build
+* [```af6958f9```](https://github.com/ktmeaton/plague-phylogeography/commit/af6958f9) snpeff and gb process doc update
+* [```5b7d08ab```](https://github.com/ktmeaton/plague-phylogeography/commit/5b7d08ab) comment out unnecessary db param
+* [```3c2625dd```](https://github.com/ktmeaton/plague-phylogeography/commit/3c2625dd) add new artifacts
+* [```5619c3c0```](https://github.com/ktmeaton/plague-phylogeography/commit/5619c3c0) remove rst lint
+* [```fb829fef```](https://github.com/ktmeaton/plague-phylogeography/commit/fb829fef) locally confirmed pipeline
+* [```547d33c2```](https://github.com/ktmeaton/plague-phylogeography/commit/547d33c2) disable rst linting
+* [```387cce80```](https://github.com/ktmeaton/plague-phylogeography/commit/387cce80) lint and actions update
+* [```020aebf8```](https://github.com/ktmeaton/plague-phylogeography/commit/020aebf8) switch snippy pairwise to gb ref
+* [```8610d388```](https://github.com/ktmeaton/plague-phylogeography/commit/8610d388) remove geopy from env
+* [```3dd58612```](https://github.com/ktmeaton/plague-phylogeography/commit/3dd58612) finish draft snpeff build db
+* [```8c78bb77```](https://github.com/ktmeaton/plague-phylogeography/commit/8c78bb77) began work on snpeff build db
+* [```e65a705e```](https://github.com/ktmeaton/plague-phylogeography/commit/e65a705e) remove rule exception
+* [```3957d6aa```](https://github.com/ktmeaton/plague-phylogeography/commit/3957d6aa) change sql queries to KEEP and EAGER
+* [```29851191```](https://github.com/ktmeaton/plague-phylogeography/commit/29851191) heading spacing
+* [```e267be00```](https://github.com/ktmeaton/plague-phylogeography/commit/e267be00) rst-lint desc
+* [```df9daeed```](https://github.com/ktmeaton/plague-phylogeography/commit/df9daeed) rst-lint desc
+* [```632cba20```](https://github.com/ktmeaton/plague-phylogeography/commit/632cba20) ignore md line length rule
+* [```a758dda2```](https://github.com/ktmeaton/plague-phylogeography/commit/a758dda2) ignore md line length rule
+* [```27a3a6ba```](https://github.com/ktmeaton/plague-phylogeography/commit/27a3a6ba) add geopy to environment
+* [```1a446665```](https://github.com/ktmeaton/plague-phylogeography/commit/1a446665) database update with new text export
+* [```d05ed718```](https://github.com/ktmeaton/plague-phylogeography/commit/d05ed718) force string conversion of values
+* [```4583752c```](https://github.com/ktmeaton/plague-phylogeography/commit/4583752c) simplify rst lint description
+* [```2d9255b4```](https://github.com/ktmeaton/plague-phylogeography/commit/2d9255b4) add rst linting to workflow
+* [```9d6b20b7```](https://github.com/ktmeaton/plague-phylogeography/commit/9d6b20b7) add rst linter
+* [```a86c6dc1```](https://github.com/ktmeaton/plague-phylogeography/commit/a86c6dc1) update ncbimeta_annotate docs
+* [```55dbb8d7```](https://github.com/ktmeaton/plague-phylogeography/commit/55dbb8d7) add export to ncbimeta_update
+* [```421639c0```](https://github.com/ktmeaton/plague-phylogeography/commit/421639c0) add markdownlint pre-commit
+* [```39d1723c```](https://github.com/ktmeaton/plague-phylogeography/commit/39d1723c) fully commented biosample
+* [```9f0d93aa```](https://github.com/ktmeaton/plague-phylogeography/commit/9f0d93aa) start the KEEP annotations
+* [```738582a0```](https://github.com/ktmeaton/plague-phylogeography/commit/738582a0) finish peru annotations
+* [```fab10f3b```](https://github.com/ktmeaton/plague-phylogeography/commit/fab10f3b) finish cui annotations
+* [```3902168a```](https://github.com/ktmeaton/plague-phylogeography/commit/3902168a) start EAGER annot and lab
+* [```ffe6bff2```](https://github.com/ktmeaton/plague-phylogeography/commit/ffe6bff2) add not yp comments
+* [```176ca2ed```](https://github.com/ktmeaton/plague-phylogeography/commit/176ca2ed) minor edit to run
+* [```0ced3ac2```](https://github.com/ktmeaton/plague-phylogeography/commit/0ced3ac2) add excutable permissions to scripts
+* [```58168974```](https://github.com/ktmeaton/plague-phylogeography/commit/58168974) any lint files
+* [```004c141a```](https://github.com/ktmeaton/plague-phylogeography/commit/004c141a) fix indentation
+* [```8e0010f5```](https://github.com/ktmeaton/plague-phylogeography/commit/8e0010f5) remove problematic name key
+* [```7a37b473```](https://github.com/ktmeaton/plague-phylogeography/commit/7a37b473) place pipeline in conda env
+* [```e4e92e63```](https://github.com/ktmeaton/plague-phylogeography/commit/e4e92e63) disable ordered list lint
+* [```5c6b1be1```](https://github.com/ktmeaton/plague-phylogeography/commit/5c6b1be1) use gh actions for conda setup
+* [```2e492865```](https://github.com/ktmeaton/plague-phylogeography/commit/2e492865) add ordered list linting
+* [```5f457292```](https://github.com/ktmeaton/plague-phylogeography/commit/5f457292) fix mixed line endings
+* [```bb534fc8```](https://github.com/ktmeaton/plague-phylogeography/commit/bb534fc8) add pipeline workflow
+* [```039463c0```](https://github.com/ktmeaton/plague-phylogeography/commit/039463c0) README linting
+* [```5329431f```](https://github.com/ktmeaton/plague-phylogeography/commit/5329431f) try restrict lint
+* [```d855191f```](https://github.com/ktmeaton/plague-phylogeography/commit/d855191f) language for fenced code block
+* [```4a2de625```](https://github.com/ktmeaton/plague-phylogeography/commit/4a2de625) lint format blanks around headings and lists
+* [```885b1d78```](https://github.com/ktmeaton/plague-phylogeography/commit/885b1d78) add markdown linting action
+* [```3bd64feb```](https://github.com/ktmeaton/plague-phylogeography/commit/3bd64feb) relocate nextstrain metadata
+* [```10380a83```](https://github.com/ktmeaton/plague-phylogeography/commit/10380a83) improved dev env instructions
+* [```c6136af8```](https://github.com/ktmeaton/plague-phylogeography/commit/c6136af8) dev dependencies and pre-commit
+* [```4d52972c```](https://github.com/ktmeaton/plague-phylogeography/commit/4d52972c) remove after rename
+* [```c9b44e4b```](https://github.com/ktmeaton/plague-phylogeography/commit/c9b44e4b) rename extension
+* [```7c884c98```](https://github.com/ktmeaton/plague-phylogeography/commit/7c884c98) update ncbimeta to remove annot file
+* [```282e4f4f```](https://github.com/ktmeaton/plague-phylogeography/commit/282e4f4f) annot remove long branch sample
+* [```5b1a8a13```](https://github.com/ktmeaton/plague-phylogeography/commit/5b1a8a13) remove the test pipeline
+* [```dc2f62a0```](https://github.com/ktmeaton/plague-phylogeography/commit/dc2f62a0) add the sed replacement
+* [```d05e19aa```](https://github.com/ktmeaton/plague-phylogeography/commit/d05e19aa) switch to new annotation format
+* [```102d8003```](https://github.com/ktmeaton/plague-phylogeography/commit/102d8003) include no data char as parameter
+* [```dd2e6c10```](https://github.com/ktmeaton/plague-phylogeography/commit/dd2e6c10) deal with unescaped quotes in annotation
+* [```caefeb45```](https://github.com/ktmeaton/plague-phylogeography/commit/caefeb45) more convoluted if skipping
+* [```2bc5ad3d```](https://github.com/ktmeaton/plague-phylogeography/commit/2bc5ad3d) incorporate ncbimeta annot if
+* [```5200f860```](https://github.com/ktmeaton/plague-phylogeography/commit/5200f860) db annot update skipping
+* [```9f83f0ea```](https://github.com/ktmeaton/plague-phylogeography/commit/9f83f0ea) misc metadata
+* [```ecb2ceaa```](https://github.com/ktmeaton/plague-phylogeography/commit/ecb2ceaa) allowing skipping
+* [```eb3223d9```](https://github.com/ktmeaton/plague-phylogeography/commit/eb3223d9) test conditional input with filename
+* [```99f8ffa0```](https://github.com/ktmeaton/plague-phylogeography/commit/99f8ffa0) additional skip variables
+* [```6d8c5921```](https://github.com/ktmeaton/plague-phylogeography/commit/6d8c5921) convoluted if statements to allow skipping
+* [```91c168d1```](https://github.com/ktmeaton/plague-phylogeography/commit/91c168d1) don't try to geocode values like missing or unknown
+* [```1c8210bd```](https://github.com/ktmeaton/plague-phylogeography/commit/1c8210bd) first draft at geocode script
+* [```b5e65a96```](https://github.com/ktmeaton/plague-phylogeography/commit/b5e65a96) commit before simplify try block
+* [```2b6484d3```](https://github.com/ktmeaton/plague-phylogeography/commit/2b6484d3) executable geocode script
+* [```a6aa2189```](https://github.com/ktmeaton/plague-phylogeography/commit/a6aa2189) script to automate geocoding
+* [```b54ffbd5```](https://github.com/ktmeaton/plague-phylogeography/commit/b54ffbd5) geocoding notes
+* [```26b2bb29```](https://github.com/ktmeaton/plague-phylogeography/commit/26b2bb29) more nextstrain edits
+* [```c1d776eb```](https://github.com/ktmeaton/plague-phylogeography/commit/c1d776eb) demo metadata files for annot and nextstrain
+* [```ac954d0c```](https://github.com/ktmeaton/plague-phylogeography/commit/ac954d0c) nextstrain metadata task
+* [```f976c927```](https://github.com/ktmeaton/plague-phylogeography/commit/f976c927) remove split col processing
+* [```6defb800```](https://github.com/ktmeaton/plague-phylogeography/commit/6defb800) last commit before give up split col
+* [```0ad71644```](https://github.com/ktmeaton/plague-phylogeography/commit/0ad71644) better db checking
+* [```9ceeef2d```](https://github.com/ktmeaton/plague-phylogeography/commit/9ceeef2d) better db file checking
+* [```22e5fb5b```](https://github.com/ktmeaton/plague-phylogeography/commit/22e5fb5b) nextstrain convert to tsv
+* [```c4664daa```](https://github.com/ktmeaton/plague-phylogeography/commit/c4664daa) v0.1.2 init changes
+* [```a2f6e9eb```](https://github.com/ktmeaton/plague-phylogeography/commit/a2f6e9eb) proper project name filtering for bronze age
+* [```2d7185e1```](https://github.com/ktmeaton/plague-phylogeography/commit/2d7185e1) space format
+* [```c036106d```](https://github.com/ktmeaton/plague-phylogeography/commit/c036106d) notes on annot db prep
+* [```8ab4472d```](https://github.com/ktmeaton/plague-phylogeography/commit/8ab4472d) Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
+* [```1ed03ce0```](https://github.com/ktmeaton/plague-phylogeography/commit/1ed03ce0) multiqc cross-ref and channels
+* [```8f12195d```](https://github.com/ktmeaton/plague-phylogeography/commit/8f12195d) qualimap cross-ref and channels
+* [```234204ad```](https://github.com/ktmeaton/plague-phylogeography/commit/234204ad) qualimap cross-ref and channels
+* [```ad7b0d99```](https://github.com/ktmeaton/plague-phylogeography/commit/ad7b0d99) include phylogeny and nextstrain pages
+* [```a058ffae```](https://github.com/ktmeaton/plague-phylogeography/commit/a058ffae) create new phylogeny and nextstrain pages
+* [```272edacb```](https://github.com/ktmeaton/plague-phylogeography/commit/272edacb) iqtree cross-ref and channels
+* [```16437718```](https://github.com/ktmeaton/plague-phylogeography/commit/16437718) snippy multi filter
+* [```2ca3eff0```](https://github.com/ktmeaton/plague-phylogeography/commit/2ca3eff0) fix bad links snippy docs
+* [```982bf8dc```](https://github.com/ktmeaton/plague-phylogeography/commit/982bf8dc) fix bad links
+* [```e6391978```](https://github.com/ktmeaton/plague-phylogeography/commit/e6391978) added snippy multi process doc
+* [```5597f551```](https://github.com/ktmeaton/plague-phylogeography/commit/5597f551) merge mask bed cross-ref and channels
+* [```ffd16aa0```](https://github.com/ktmeaton/plague-phylogeography/commit/ffd16aa0) snp density cross-ref and channels
+* [```a18c4f1a```](https://github.com/ktmeaton/plague-phylogeography/commit/a18c4f1a) remove unnecessary variant summary process
+* [```77dd6b76```](https://github.com/ktmeaton/plague-phylogeography/commit/77dd6b76) commit before variant summary collect rewrite
+* [```e2adfdf4```](https://github.com/ktmeaton/plague-phylogeography/commit/e2adfdf4) variant summary ch and cross-ref
+* [```5db4635e```](https://github.com/ktmeaton/plague-phylogeography/commit/5db4635e) add bam to pairwise snippy doc publish
+* [```d05278b6```](https://github.com/ktmeaton/plague-phylogeography/commit/d05278b6) pairwise snippy cross-ref, channels, script
+* [```5a826c2e```](https://github.com/ktmeaton/plague-phylogeography/commit/5a826c2e) New KEEP to BioSample and Master
+* [```a0b7700b```](https://github.com/ktmeaton/plague-phylogeography/commit/a0b7700b) low complexity cross-ref and channel
+* [```fd7dc07c```](https://github.com/ktmeaton/plague-phylogeography/commit/fd7dc07c) detect repeats cross-ref and publish update
+* [```4e1ecc21```](https://github.com/ktmeaton/plague-phylogeography/commit/4e1ecc21) update shell script and cross-ref
+* [```543e01a9```](https://github.com/ktmeaton/plague-phylogeography/commit/543e01a9) make ref fasta editing generic to match gb
+* [```beb569cb```](https://github.com/ktmeaton/plague-phylogeography/commit/beb569cb) note automate snpeff tbd
+* [```face7267```](https://github.com/ktmeaton/plague-phylogeography/commit/face7267) update assembly cross-ref
+* [```d1567afb```](https://github.com/ktmeaton/plague-phylogeography/commit/d1567afb) update descriptions and channels
+* [```d713d24c```](https://github.com/ktmeaton/plague-phylogeography/commit/d713d24c) eager params and new sqlite query
+* [```f82390f2```](https://github.com/ktmeaton/plague-phylogeography/commit/f82390f2) use script to prep SRA metadata for EAGER tsv
+* [```58eaf5b9```](https://github.com/ktmeaton/plague-phylogeography/commit/58eaf5b9) allow --max-datasets as parameter
+* [```658a58f8```](https://github.com/ktmeaton/plague-phylogeography/commit/658a58f8) update description and help commands
+* [```56584fca```](https://github.com/ktmeaton/plague-phylogeography/commit/56584fca) script to prep EAGER tsv input from sqlite
+* [```1a5a6b3d```](https://github.com/ktmeaton/plague-phylogeography/commit/1a5a6b3d) update docs and add process cross-ref
+* [```55e07929```](https://github.com/ktmeaton/plague-phylogeography/commit/55e07929) add sphinx extension for cross ref
+* [```ea86c37e```](https://github.com/ktmeaton/plague-phylogeography/commit/ea86c37e) remove h1 header from title
+* [```b48fc317```](https://github.com/ktmeaton/plague-phylogeography/commit/b48fc317) fix ref 8
+* [```cd2f2668```](https://github.com/ktmeaton/plague-phylogeography/commit/cd2f2668) reference rearrange (1-11)
+* [```9a17930e```](https://github.com/ktmeaton/plague-phylogeography/commit/9a17930e) heading size in abstract
+* [```90f835f3```](https://github.com/ktmeaton/plague-phylogeography/commit/90f835f3) title simplify more
+* [```6821caf8```](https://github.com/ktmeaton/plague-phylogeography/commit/6821caf8) explain Swedish finding significance
+* [```e0b2cf81```](https://github.com/ktmeaton/plague-phylogeography/commit/e0b2cf81) modern dna to ancient transition
+* [```57f46cff```](https://github.com/ktmeaton/plague-phylogeography/commit/57f46cff) fix restart animation link
+* [```67248842```](https://github.com/ktmeaton/plague-phylogeography/commit/67248842) origins dna update
+* [```ed052b4e```](https://github.com/ktmeaton/plague-phylogeography/commit/ed052b4e) simplified titles
+* [```234de861```](https://github.com/ktmeaton/plague-phylogeography/commit/234de861) minor grammar
+* [```84540577```](https://github.com/ktmeaton/plague-phylogeography/commit/84540577) remove iconic maps section
+* [```a022e2f9```](https://github.com/ktmeaton/plague-phylogeography/commit/a022e2f9) explain reconstruction
+* [```2b1cf708```](https://github.com/ktmeaton/plague-phylogeography/commit/2b1cf708) rearrange
+* [```adac8af9```](https://github.com/ktmeaton/plague-phylogeography/commit/adac8af9) origins edits
+* [```436bad01```](https://github.com/ktmeaton/plague-phylogeography/commit/436bad01) center justify left side text links
+* [```ed31b70e```](https://github.com/ktmeaton/plague-phylogeography/commit/ed31b70e) remove test commands (SUCCESS)
+* [```3264277f```](https://github.com/ktmeaton/plague-phylogeography/commit/3264277f) test remote change with heading
+* [```a9bf5f04```](https://github.com/ktmeaton/plague-phylogeography/commit/a9bf5f04) try p tag outside of abstract
+* [```b5e2da1a```](https://github.com/ktmeaton/plague-phylogeography/commit/b5e2da1a) CSS remote test 2
+* [```f1a85316```](https://github.com/ktmeaton/plague-phylogeography/commit/f1a85316) CSS Override Remote?
+* [```1607405f```](https://github.com/ktmeaton/plague-phylogeography/commit/1607405f) CSS Override
+* [```2b11bafc```](https://github.com/ktmeaton/plague-phylogeography/commit/2b11bafc) remove the DemoMap test
+* [```2a50b974```](https://github.com/ktmeaton/plague-phylogeography/commit/2a50b974) correct heading size
+* [```96e13cad```](https://github.com/ktmeaton/plague-phylogeography/commit/96e13cad) github actions reminder
+* [```37e452dc```](https://github.com/ktmeaton/plague-phylogeography/commit/37e452dc) switch all bold md to html tags
+* [```61af328e```](https://github.com/ktmeaton/plague-phylogeography/commit/61af328e) accept cmd line args
+* [```8862bb80```](https://github.com/ktmeaton/plague-phylogeography/commit/8862bb80) test html bold tag
+* [```f5603191```](https://github.com/ktmeaton/plague-phylogeography/commit/f5603191) writing edits and autogen
+* [```79c048c2```](https://github.com/ktmeaton/plague-phylogeography/commit/79c048c2) script to convert local to remote
+* [```431d8304```](https://github.com/ktmeaton/plague-phylogeography/commit/431d8304) bolding and tidying
+* [```2d07feb7```](https://github.com/ktmeaton/plague-phylogeography/commit/2d07feb7) all bib items updated
+* [```259e44bf```](https://github.com/ktmeaton/plague-phylogeography/commit/259e44bf) bib up to origins ancient dna
+* [```ba9311bd```](https://github.com/ktmeaton/plague-phylogeography/commit/ba9311bd) bib up to origins history
+* [```0bd7c80d```](https://github.com/ktmeaton/plague-phylogeography/commit/0bd7c80d) started footnote style
+* [```924d49b6```](https://github.com/ktmeaton/plague-phylogeography/commit/924d49b6) switch to superscript reference
+* [```194c8cc4```](https://github.com/ktmeaton/plague-phylogeography/commit/194c8cc4) add local specifier
+* [```040b9147```](https://github.com/ktmeaton/plague-phylogeography/commit/040b9147) breka up long sentence
+* [```e2b205a4```](https://github.com/ktmeaton/plague-phylogeography/commit/e2b205a4) wording area vs lineages
+* [```83c91bea```](https://github.com/ktmeaton/plague-phylogeography/commit/83c91bea) rename to repo prefix
+* [```d9ca1013```](https://github.com/ktmeaton/plague-phylogeography/commit/d9ca1013) plague SCDS 2020 remote narrative
+* [```f9bb4077```](https://github.com/ktmeaton/plague-phylogeography/commit/f9bb4077) before remote switch
+* [```91588975```](https://github.com/ktmeaton/plague-phylogeography/commit/91588975) add table of contents
 
 ## v0.1.1
 
 ### Commits
 
-* [```7af1c44```](https://github.com/ktmeaton/plague-phylogeography/commit/7af1c44) add bash to all code blocks
-* [```25d071d```](https://github.com/ktmeaton/plague-phylogeography/commit/25d071d) revert back to code bash
-* [```c400d53```](https://github.com/ktmeaton/plague-phylogeography/commit/c400d53) replace code block with shell script
-* [```a51bfe0```](https://github.com/ktmeaton/plague-phylogeography/commit/a51bfe0) add pygments style
-* [```7dc5929```](https://github.com/ktmeaton/plague-phylogeography/commit/7dc5929) simplified docs rst
-* [```ff67bfd```](https://github.com/ktmeaton/plague-phylogeography/commit/ff67bfd) split README into notes file
-* [```81d9358```](https://github.com/ktmeaton/plague-phylogeography/commit/81d9358) v0.1.1 updates
-* [```ede6f6d```](https://github.com/ktmeaton/plague-phylogeography/commit/ede6f6d) digital scholarship wrap up
-* [```6dfae28```](https://github.com/ktmeaton/plague-phylogeography/commit/6dfae28) rename to plague phylo
-* [```e89a226```](https://github.com/ktmeaton/plague-phylogeography/commit/e89a226) one-liner dev depend
-* [```49a5504```](https://github.com/ktmeaton/plague-phylogeography/commit/49a5504) set master doc to index
-* [```2de0f1d```](https://github.com/ktmeaton/plague-phylogeography/commit/2de0f1d) fix underline
-* [```34e357e```](https://github.com/ktmeaton/plague-phylogeography/commit/34e357e) human ecology
-* [```0260851```](https://github.com/ktmeaton/plague-phylogeography/commit/0260851) edit docs pages
-* [```a215a76```](https://github.com/ktmeaton/plague-phylogeography/commit/a215a76) ecology 1
-* [```73049d7```](https://github.com/ktmeaton/plague-phylogeography/commit/73049d7) time vortex slide
-* [```660ff5f```](https://github.com/ktmeaton/plague-phylogeography/commit/660ff5f) before splitting aDNA
-* [```28df1e1```](https://github.com/ktmeaton/plague-phylogeography/commit/28df1e1) neolithic map
-* [```3c43195```](https://github.com/ktmeaton/plague-phylogeography/commit/3c43195) commit before neolithic swap
-* [```cf6059b```](https://github.com/ktmeaton/plague-phylogeography/commit/cf6059b) images rename and backup
-* [```7e80772```](https://github.com/ktmeaton/plague-phylogeography/commit/7e80772) skeleton and map pic
-* [```2696a8d```](https://github.com/ktmeaton/plague-phylogeography/commit/2696a8d) origins text historical
-* [```b7fd8ee```](https://github.com/ktmeaton/plague-phylogeography/commit/b7fd8ee) draft of the 7 slide viz
-* [```91aec7a```](https://github.com/ktmeaton/plague-phylogeography/commit/91aec7a) SCDS 2020 Visualization narrative
-* [```3521a02```](https://github.com/ktmeaton/plague-phylogeography/commit/3521a02) ignore the test150 dir
-* [```732e832```](https://github.com/ktmeaton/plague-phylogeography/commit/732e832) human and what's next
-* [```7814b8f```](https://github.com/ktmeaton/plague-phylogeography/commit/7814b8f) ecology writing
-* [```245df6c```](https://github.com/ktmeaton/plague-phylogeography/commit/245df6c) rearrange and new time content
-* [```1320444```](https://github.com/ktmeaton/plague-phylogeography/commit/1320444) 150 to 200
-* [```938d67c```](https://github.com/ktmeaton/plague-phylogeography/commit/938d67c) 90 tp 150
-* [```7e541a4```](https://github.com/ktmeaton/plague-phylogeography/commit/7e541a4) 100 to 90
-* [```63c31d2```](https://github.com/ktmeaton/plague-phylogeography/commit/63c31d2) put div in left
-* [```38ba984```](https://github.com/ktmeaton/plague-phylogeography/commit/38ba984) plague img
-* [```f004d58```](https://github.com/ktmeaton/plague-phylogeography/commit/f004d58) test reset
-* [```bc81aa4```](https://github.com/ktmeaton/plague-phylogeography/commit/bc81aa4) resize 200 to 100
-* [```57f870c```](https://github.com/ktmeaton/plague-phylogeography/commit/57f870c) replace image and resize
-* [```e7abcec```](https://github.com/ktmeaton/plague-phylogeography/commit/e7abcec) right text test again
-* [```c1b3b86```](https://github.com/ktmeaton/plague-phylogeography/commit/c1b3b86) test reset
-* [```b8a51d9```](https://github.com/ktmeaton/plague-phylogeography/commit/b8a51d9) 400 to 100
-* [```624b2b8```](https://github.com/ktmeaton/plague-phylogeography/commit/624b2b8) truncate
-* [```347033b```](https://github.com/ktmeaton/plague-phylogeography/commit/347033b) size 100 to 400
-* [```2f6b671```](https://github.com/ktmeaton/plague-phylogeography/commit/2f6b671) test change
-* [```2127a43```](https://github.com/ktmeaton/plague-phylogeography/commit/2127a43) add header to right size
-* [```1068cab```](https://github.com/ktmeaton/plague-phylogeography/commit/1068cab) geo compare
-* [```94f0328```](https://github.com/ktmeaton/plague-phylogeography/commit/94f0328) img test
-* [```0670ce2```](https://github.com/ktmeaton/plague-phylogeography/commit/0670ce2) spacing experiment 3
-* [```0ecbcb7```](https://github.com/ktmeaton/plague-phylogeography/commit/0ecbcb7) spacing experiment 2
-* [```09ca8c6```](https://github.com/ktmeaton/plague-phylogeography/commit/09ca8c6) spacing experiment
-* [```f300955```](https://github.com/ktmeaton/plague-phylogeography/commit/f300955) new geographic spread
-* [```19c1bc7```](https://github.com/ktmeaton/plague-phylogeography/commit/19c1bc7) new abstract
-* [```8c7b146```](https://github.com/ktmeaton/plague-phylogeography/commit/8c7b146) some export change
-* [```a50c665```](https://github.com/ktmeaton/plague-phylogeography/commit/a50c665) spread rearrange
-* [```c2d72d7```](https://github.com/ktmeaton/plague-phylogeography/commit/c2d72d7) switch all Local links to Remote
-* [```d11e0b5```](https://github.com/ktmeaton/plague-phylogeography/commit/d11e0b5) try to sync remote narrative
-* [```2621a9a```](https://github.com/ktmeaton/plague-phylogeography/commit/2621a9a) big narrative change for local
-* [```19f66bb```](https://github.com/ktmeaton/plague-phylogeography/commit/19f66bb) focus remote on map
-* [```cc1a7b0```](https://github.com/ktmeaton/plague-phylogeography/commit/cc1a7b0) fix links again
-* [```953223d```](https://github.com/ktmeaton/plague-phylogeography/commit/953223d) clarify auspice remote local names
-* [```3065c4a```](https://github.com/ktmeaton/plague-phylogeography/commit/3065c4a) delete poorly named files
-* [```3031d1b```](https://github.com/ktmeaton/plague-phylogeography/commit/3031d1b) clarify remote local names
-* [```3e73271```](https://github.com/ktmeaton/plague-phylogeography/commit/3e73271) fix remote and local url
-* [```f8a3bf4```](https://github.com/ktmeaton/plague-phylogeography/commit/f8a3bf4) add remote links test
-* [```881cecd```](https://github.com/ktmeaton/plague-phylogeography/commit/881cecd) rename and del
-* [```01bb89d```](https://github.com/ktmeaton/plague-phylogeography/commit/01bb89d) fix typo
-* [```22812e0```](https://github.com/ktmeaton/plague-phylogeography/commit/22812e0) narratives update for server deploy
-* [```303a66b```](https://github.com/ktmeaton/plague-phylogeography/commit/303a66b) notes to successfully run the plague150 nextstrain
-* [```21729d3```](https://github.com/ktmeaton/plague-phylogeography/commit/21729d3) remove testing ncov narrative
-* [```9340c4f```](https://github.com/ktmeaton/plague-phylogeography/commit/9340c4f) make copy of plague150 for nextstrain community
-* [```4f3f2e2```](https://github.com/ktmeaton/plague-phylogeography/commit/4f3f2e2) function plague150 auspice!
-* [```a04876b```](https://github.com/ktmeaton/plague-phylogeography/commit/a04876b) copy the DemoMap for local deploy
-* [```40e5287```](https://github.com/ktmeaton/plague-phylogeography/commit/40e5287) test with ncov narrative
-* [```1b44f63```](https://github.com/ktmeaton/plague-phylogeography/commit/1b44f63) first narrative Demo
-* [```81aee29```](https://github.com/ktmeaton/plague-phylogeography/commit/81aee29) try underscore
-* [```96110b9```](https://github.com/ktmeaton/plague-phylogeography/commit/96110b9) json fix
-* [```4cfb2bd```](https://github.com/ktmeaton/plague-phylogeography/commit/4cfb2bd) extra json
-* [```f459b95```](https://github.com/ktmeaton/plague-phylogeography/commit/f459b95) rename to Demomap
-* [```7fbfb4f```](https://github.com/ktmeaton/plague-phylogeography/commit/7fbfb4f) demo now with map
-* [```0ed0a1d```](https://github.com/ktmeaton/plague-phylogeography/commit/0ed0a1d) add small 150 plague
-* [```ede9cff```](https://github.com/ktmeaton/plague-phylogeography/commit/ede9cff) attempt a small build
-* [```323508b```](https://github.com/ktmeaton/plague-phylogeography/commit/323508b) remove old demo name file
-* [```edf3d13```](https://github.com/ktmeaton/plague-phylogeography/commit/edf3d13) rename demo json
-* [```988ee9a```](https://github.com/ktmeaton/plague-phylogeography/commit/988ee9a) add auspice plague demo
-* [```f6a6a0e```](https://github.com/ktmeaton/plague-phylogeography/commit/f6a6a0e) replace spaces with tabs
-* [```2d4568d```](https://github.com/ktmeaton/plague-phylogeography/commit/2d4568d) add default lat long file
-* [```b039621```](https://github.com/ktmeaton/plague-phylogeography/commit/b039621) add auspice config
-* [```f2dcf65```](https://github.com/ktmeaton/plague-phylogeography/commit/f2dcf65) nextstrain augur and auspice commands
-* [```64c6908```](https://github.com/ktmeaton/plague-phylogeography/commit/64c6908) auspice default config
-* [```a0ff343```](https://github.com/ktmeaton/plague-phylogeography/commit/a0ff343) new nextstrain metadata
-* [```e0c3358```](https://github.com/ktmeaton/plague-phylogeography/commit/e0c3358) save all bed and fasta after separating locus
-* [```50e1ed3```](https://github.com/ktmeaton/plague-phylogeography/commit/50e1ed3) Index update
-* [```e6d7994```](https://github.com/ktmeaton/plague-phylogeography/commit/e6d7994) fix output to CHROM
-* [```89db81b```](https://github.com/ktmeaton/plague-phylogeography/commit/89db81b) demo plague json for auspice
-* [```614af0f```](https://github.com/ktmeaton/plague-phylogeography/commit/614af0f) updates and EOF testing
-* [```3ed0a7f```](https://github.com/ktmeaton/plague-phylogeography/commit/3ed0a7f) new command to eliminate missing geo
-* [```3ffa84b```](https://github.com/ktmeaton/plague-phylogeography/commit/3ffa84b) snippy_multi_filter now only uses chromosome coords
-* [```9018d38```](https://github.com/ktmeaton/plague-phylogeography/commit/9018d38) discard nextstrain output
-* [```81d8cf6```](https://github.com/ktmeaton/plague-phylogeography/commit/81d8cf6) rename to split locus
-* [```cb2969b```](https://github.com/ktmeaton/plague-phylogeography/commit/cb2969b) better file naming
-* [```ff907cc```](https://github.com/ktmeaton/plague-phylogeography/commit/ff907cc) cleanup and reorganize
-* [```bdde729```](https://github.com/ktmeaton/plague-phylogeography/commit/bdde729) update snippy to v.4.6.0
-* [```779fe10```](https://github.com/ktmeaton/plague-phylogeography/commit/779fe10) ignore nextstrain output for now
-* [```7981226```](https://github.com/ktmeaton/plague-phylogeography/commit/7981226) actual eager param
-* [```8edd221```](https://github.com/ktmeaton/plague-phylogeography/commit/8edd221) just chromosome gb
-* [```3619c44```](https://github.com/ktmeaton/plague-phylogeography/commit/3619c44) extra metadata
-* [```71a246c```](https://github.com/ktmeaton/plague-phylogeography/commit/71a246c) commit possible db changes
-* [```114450b```](https://github.com/ktmeaton/plague-phylogeography/commit/114450b) visualize results
-* [```30d401c```](https://github.com/ktmeaton/plague-phylogeography/commit/30d401c) geocoding for lat lon
-* [```5186ba6```](https://github.com/ktmeaton/plague-phylogeography/commit/5186ba6) Infer ancestral seq
-* [```d9fd574```](https://github.com/ktmeaton/plague-phylogeography/commit/d9fd574) timetree refine branch lengths
-* [```69b6130```](https://github.com/ktmeaton/plague-phylogeography/commit/69b6130) nextstrain refine and metadata
-* [```a571079```](https://github.com/ktmeaton/plague-phylogeography/commit/a571079) nextstrain installation and environment
-* [```09ec15f```](https://github.com/ktmeaton/plague-phylogeography/commit/09ec15f) env update typo fix
-* [```a27be8c```](https://github.com/ktmeaton/plague-phylogeography/commit/a27be8c) eager header
-* [```7409909```](https://github.com/ktmeaton/plague-phylogeography/commit/7409909) move eager test files to new dir
-* [```bca2fc5```](https://github.com/ktmeaton/plague-phylogeography/commit/bca2fc5) test SRA input to eager
-* [```5e1a724```](https://github.com/ktmeaton/plague-phylogeography/commit/5e1a724) RAEDNE EAGER setup
-* [```4784bd3```](https://github.com/ktmeaton/plague-phylogeography/commit/4784bd3) eager tsv input instructions
-* [```3bb3074```](https://github.com/ktmeaton/plague-phylogeography/commit/3bb3074) change mask char to X!
-* [```a4ce275```](https://github.com/ktmeaton/plague-phylogeography/commit/a4ce275) Notes about adding more repeat masking
-* [```1e27c3c```](https://github.com/ktmeaton/plague-phylogeography/commit/1e27c3c) being sra for download
-* [```63ac9e0```](https://github.com/ktmeaton/plague-phylogeography/commit/63ac9e0) test bronze age sra select
-* [```72831be```](https://github.com/ktmeaton/plague-phylogeography/commit/72831be) test sra sqlite select
-* [```63b6e59```](https://github.com/ktmeaton/plague-phylogeography/commit/63b6e59) add Rise of the Bronze Age project to BioSample search
-* [```44d54fe```](https://github.com/ktmeaton/plague-phylogeography/commit/44d54fe) remove modeltest-ng from dependencies
-* [```62dce50```](https://github.com/ktmeaton/plague-phylogeography/commit/62dce50) new db after pairwise aln filter
-* [```41ae09e```](https://github.com/ktmeaton/plague-phylogeography/commit/41ae09e) drop master join tables before new join
-* [```affb1c0```](https://github.com/ktmeaton/plague-phylogeography/commit/affb1c0) doc modelfinder changes
-* [```1e4897a```](https://github.com/ktmeaton/plague-phylogeography/commit/1e4897a) pairwise align filter
-* [```8771033```](https://github.com/ktmeaton/plague-phylogeography/commit/8771033) remove modeltest-ng use modelfinder instead
-* [```e9d7d8d```](https://github.com/ktmeaton/plague-phylogeography/commit/e9d7d8d) fix compare repo and commits
+* [```7af1c44b```](https://github.com/ktmeaton/plague-phylogeography/commit/7af1c44b) add bash to all code blocks
+* [```25d071d9```](https://github.com/ktmeaton/plague-phylogeography/commit/25d071d9) revert back to code bash
+* [```c400d533```](https://github.com/ktmeaton/plague-phylogeography/commit/c400d533) replace code block with shell script
+* [```a51bfe0f```](https://github.com/ktmeaton/plague-phylogeography/commit/a51bfe0f) add pygments style
+* [```7dc59290```](https://github.com/ktmeaton/plague-phylogeography/commit/7dc59290) simplified docs rst
+* [```ff67bfdb```](https://github.com/ktmeaton/plague-phylogeography/commit/ff67bfdb) split README into notes file
+* [```81d93580```](https://github.com/ktmeaton/plague-phylogeography/commit/81d93580) v0.1.1 updates
+* [```ede6f6d5```](https://github.com/ktmeaton/plague-phylogeography/commit/ede6f6d5) digital scholarship wrap up
+* [```6dfae28c```](https://github.com/ktmeaton/plague-phylogeography/commit/6dfae28c) rename to plague phylo
+* [```e89a2269```](https://github.com/ktmeaton/plague-phylogeography/commit/e89a2269) one-liner dev depend
+* [```49a5504a```](https://github.com/ktmeaton/plague-phylogeography/commit/49a5504a) set master doc to index
+* [```2de0f1db```](https://github.com/ktmeaton/plague-phylogeography/commit/2de0f1db) fix underline
+* [```34e357ec```](https://github.com/ktmeaton/plague-phylogeography/commit/34e357ec) human ecology
+* [```02608513```](https://github.com/ktmeaton/plague-phylogeography/commit/02608513) edit docs pages
+* [```a215a766```](https://github.com/ktmeaton/plague-phylogeography/commit/a215a766) ecology 1
+* [```73049d76```](https://github.com/ktmeaton/plague-phylogeography/commit/73049d76) time vortex slide
+* [```660ff5f1```](https://github.com/ktmeaton/plague-phylogeography/commit/660ff5f1) before splitting aDNA
+* [```28df1e1c```](https://github.com/ktmeaton/plague-phylogeography/commit/28df1e1c) neolithic map
+* [```3c43195d```](https://github.com/ktmeaton/plague-phylogeography/commit/3c43195d) commit before neolithic swap
+* [```cf6059b1```](https://github.com/ktmeaton/plague-phylogeography/commit/cf6059b1) images rename and backup
+* [```7e80772d```](https://github.com/ktmeaton/plague-phylogeography/commit/7e80772d) skeleton and map pic
+* [```2696a8d1```](https://github.com/ktmeaton/plague-phylogeography/commit/2696a8d1) origins text historical
+* [```b7fd8eed```](https://github.com/ktmeaton/plague-phylogeography/commit/b7fd8eed) draft of the 7 slide viz
+* [```91aec7a6```](https://github.com/ktmeaton/plague-phylogeography/commit/91aec7a6) SCDS 2020 Visualization narrative
+* [```3521a020```](https://github.com/ktmeaton/plague-phylogeography/commit/3521a020) ignore the test150 dir
+* [```732e8329```](https://github.com/ktmeaton/plague-phylogeography/commit/732e8329) human and what's next
+* [```7814b8f6```](https://github.com/ktmeaton/plague-phylogeography/commit/7814b8f6) ecology writing
+* [```245df6cb```](https://github.com/ktmeaton/plague-phylogeography/commit/245df6cb) rearrange and new time content
+* [```13204449```](https://github.com/ktmeaton/plague-phylogeography/commit/13204449) 150 to 200
+* [```938d67c3```](https://github.com/ktmeaton/plague-phylogeography/commit/938d67c3) 90 tp 150
+* [```7e541a46```](https://github.com/ktmeaton/plague-phylogeography/commit/7e541a46) 100 to 90
+* [```63c31d23```](https://github.com/ktmeaton/plague-phylogeography/commit/63c31d23) put div in left
+* [```38ba984f```](https://github.com/ktmeaton/plague-phylogeography/commit/38ba984f) plague img
+* [```f004d58b```](https://github.com/ktmeaton/plague-phylogeography/commit/f004d58b) test reset
+* [```bc81aa4d```](https://github.com/ktmeaton/plague-phylogeography/commit/bc81aa4d) resize 200 to 100
+* [```57f870cc```](https://github.com/ktmeaton/plague-phylogeography/commit/57f870cc) replace image and resize
+* [```e7abcecd```](https://github.com/ktmeaton/plague-phylogeography/commit/e7abcecd) right text test again
+* [```c1b3b868```](https://github.com/ktmeaton/plague-phylogeography/commit/c1b3b868) test reset
+* [```b8a51d9c```](https://github.com/ktmeaton/plague-phylogeography/commit/b8a51d9c) 400 to 100
+* [```624b2b8f```](https://github.com/ktmeaton/plague-phylogeography/commit/624b2b8f) truncate
+* [```347033bb```](https://github.com/ktmeaton/plague-phylogeography/commit/347033bb) size 100 to 400
+* [```2f6b6714```](https://github.com/ktmeaton/plague-phylogeography/commit/2f6b6714) test change
+* [```2127a436```](https://github.com/ktmeaton/plague-phylogeography/commit/2127a436) add header to right size
+* [```1068cab4```](https://github.com/ktmeaton/plague-phylogeography/commit/1068cab4) geo compare
+* [```94f0328d```](https://github.com/ktmeaton/plague-phylogeography/commit/94f0328d) img test
+* [```0670ce25```](https://github.com/ktmeaton/plague-phylogeography/commit/0670ce25) spacing experiment 3
+* [```0ecbcb7a```](https://github.com/ktmeaton/plague-phylogeography/commit/0ecbcb7a) spacing experiment 2
+* [```09ca8c60```](https://github.com/ktmeaton/plague-phylogeography/commit/09ca8c60) spacing experiment
+* [```f3009559```](https://github.com/ktmeaton/plague-phylogeography/commit/f3009559) new geographic spread
+* [```19c1bc7f```](https://github.com/ktmeaton/plague-phylogeography/commit/19c1bc7f) new abstract
+* [```8c7b1467```](https://github.com/ktmeaton/plague-phylogeography/commit/8c7b1467) some export change
+* [```a50c665a```](https://github.com/ktmeaton/plague-phylogeography/commit/a50c665a) spread rearrange
+* [```c2d72d70```](https://github.com/ktmeaton/plague-phylogeography/commit/c2d72d70) switch all Local links to Remote
+* [```d11e0b57```](https://github.com/ktmeaton/plague-phylogeography/commit/d11e0b57) try to sync remote narrative
+* [```2621a9a0```](https://github.com/ktmeaton/plague-phylogeography/commit/2621a9a0) big narrative change for local
+* [```19f66bb5```](https://github.com/ktmeaton/plague-phylogeography/commit/19f66bb5) focus remote on map
+* [```cc1a7b0e```](https://github.com/ktmeaton/plague-phylogeography/commit/cc1a7b0e) fix links again
+* [```953223db```](https://github.com/ktmeaton/plague-phylogeography/commit/953223db) clarify auspice remote local names
+* [```3065c4a5```](https://github.com/ktmeaton/plague-phylogeography/commit/3065c4a5) delete poorly named files
+* [```3031d1b1```](https://github.com/ktmeaton/plague-phylogeography/commit/3031d1b1) clarify remote local names
+* [```3e73271b```](https://github.com/ktmeaton/plague-phylogeography/commit/3e73271b) fix remote and local url
+* [```f8a3bf41```](https://github.com/ktmeaton/plague-phylogeography/commit/f8a3bf41) add remote links test
+* [```881cecda```](https://github.com/ktmeaton/plague-phylogeography/commit/881cecda) rename and del
+* [```01bb89d8```](https://github.com/ktmeaton/plague-phylogeography/commit/01bb89d8) fix typo
+* [```22812e0c```](https://github.com/ktmeaton/plague-phylogeography/commit/22812e0c) narratives update for server deploy
+* [```303a66be```](https://github.com/ktmeaton/plague-phylogeography/commit/303a66be) notes to successfully run the plague150 nextstrain
+* [```21729d36```](https://github.com/ktmeaton/plague-phylogeography/commit/21729d36) remove testing ncov narrative
+* [```9340c4fe```](https://github.com/ktmeaton/plague-phylogeography/commit/9340c4fe) make copy of plague150 for nextstrain community
+* [```4f3f2e25```](https://github.com/ktmeaton/plague-phylogeography/commit/4f3f2e25) function plague150 auspice!
+* [```a04876ba```](https://github.com/ktmeaton/plague-phylogeography/commit/a04876ba) copy the DemoMap for local deploy
+* [```40e5287d```](https://github.com/ktmeaton/plague-phylogeography/commit/40e5287d) test with ncov narrative
+* [```1b44f631```](https://github.com/ktmeaton/plague-phylogeography/commit/1b44f631) first narrative Demo
+* [```81aee291```](https://github.com/ktmeaton/plague-phylogeography/commit/81aee291) try underscore
+* [```96110b98```](https://github.com/ktmeaton/plague-phylogeography/commit/96110b98) json fix
+* [```4cfb2bd7```](https://github.com/ktmeaton/plague-phylogeography/commit/4cfb2bd7) extra json
+* [```f459b95a```](https://github.com/ktmeaton/plague-phylogeography/commit/f459b95a) rename to Demomap
+* [```7fbfb4fb```](https://github.com/ktmeaton/plague-phylogeography/commit/7fbfb4fb) demo now with map
+* [```0ed0a1da```](https://github.com/ktmeaton/plague-phylogeography/commit/0ed0a1da) add small 150 plague
+* [```ede9cff3```](https://github.com/ktmeaton/plague-phylogeography/commit/ede9cff3) attempt a small build
+* [```323508b2```](https://github.com/ktmeaton/plague-phylogeography/commit/323508b2) remove old demo name file
+* [```edf3d13e```](https://github.com/ktmeaton/plague-phylogeography/commit/edf3d13e) rename demo json
+* [```988ee9ae```](https://github.com/ktmeaton/plague-phylogeography/commit/988ee9ae) add auspice plague demo
+* [```f6a6a0ed```](https://github.com/ktmeaton/plague-phylogeography/commit/f6a6a0ed) replace spaces with tabs
+* [```2d4568d7```](https://github.com/ktmeaton/plague-phylogeography/commit/2d4568d7) add default lat long file
+* [```b039621b```](https://github.com/ktmeaton/plague-phylogeography/commit/b039621b) add auspice config
+* [```f2dcf65a```](https://github.com/ktmeaton/plague-phylogeography/commit/f2dcf65a) nextstrain augur and auspice commands
+* [```64c69087```](https://github.com/ktmeaton/plague-phylogeography/commit/64c69087) auspice default config
+* [```a0ff343b```](https://github.com/ktmeaton/plague-phylogeography/commit/a0ff343b) new nextstrain metadata
+* [```e0c33589```](https://github.com/ktmeaton/plague-phylogeography/commit/e0c33589) save all bed and fasta after separating locus
+* [```50e1ed33```](https://github.com/ktmeaton/plague-phylogeography/commit/50e1ed33) Index update
+* [```e6d79941```](https://github.com/ktmeaton/plague-phylogeography/commit/e6d79941) fix output to CHROM
+* [```89db81b3```](https://github.com/ktmeaton/plague-phylogeography/commit/89db81b3) demo plague json for auspice
+* [```614af0f8```](https://github.com/ktmeaton/plague-phylogeography/commit/614af0f8) updates and EOF testing
+* [```3ed0a7f1```](https://github.com/ktmeaton/plague-phylogeography/commit/3ed0a7f1) new command to eliminate missing geo
+* [```3ffa84b4```](https://github.com/ktmeaton/plague-phylogeography/commit/3ffa84b4) snippy_multi_filter now only uses chromosome coords
+* [```9018d385```](https://github.com/ktmeaton/plague-phylogeography/commit/9018d385) discard nextstrain output
+* [```81d8cf67```](https://github.com/ktmeaton/plague-phylogeography/commit/81d8cf67) rename to split locus
+* [```cb2969bc```](https://github.com/ktmeaton/plague-phylogeography/commit/cb2969bc) better file naming
+* [```ff907cc6```](https://github.com/ktmeaton/plague-phylogeography/commit/ff907cc6) cleanup and reorganize
+* [```bdde7299```](https://github.com/ktmeaton/plague-phylogeography/commit/bdde7299) update snippy to v.4.6.0
+* [```779fe10f```](https://github.com/ktmeaton/plague-phylogeography/commit/779fe10f) ignore nextstrain output for now
+* [```79812269```](https://github.com/ktmeaton/plague-phylogeography/commit/79812269) actual eager param
+* [```8edd221b```](https://github.com/ktmeaton/plague-phylogeography/commit/8edd221b) just chromosome gb
+* [```3619c44d```](https://github.com/ktmeaton/plague-phylogeography/commit/3619c44d) extra metadata
+* [```71a246cc```](https://github.com/ktmeaton/plague-phylogeography/commit/71a246cc) commit possible db changes
+* [```114450b9```](https://github.com/ktmeaton/plague-phylogeography/commit/114450b9) visualize results
+* [```30d401c3```](https://github.com/ktmeaton/plague-phylogeography/commit/30d401c3) geocoding for lat lon
+* [```5186ba68```](https://github.com/ktmeaton/plague-phylogeography/commit/5186ba68) Infer ancestral seq
+* [```d9fd5747```](https://github.com/ktmeaton/plague-phylogeography/commit/d9fd5747) timetree refine branch lengths
+* [```69b61308```](https://github.com/ktmeaton/plague-phylogeography/commit/69b61308) nextstrain refine and metadata
+* [```a571079b```](https://github.com/ktmeaton/plague-phylogeography/commit/a571079b) nextstrain installation and environment
+* [```09ec15f6```](https://github.com/ktmeaton/plague-phylogeography/commit/09ec15f6) env update typo fix
+* [```a27be8cd```](https://github.com/ktmeaton/plague-phylogeography/commit/a27be8cd) eager header
+* [```74099090```](https://github.com/ktmeaton/plague-phylogeography/commit/74099090) move eager test files to new dir
+* [```bca2fc5b```](https://github.com/ktmeaton/plague-phylogeography/commit/bca2fc5b) test SRA input to eager
+* [```5e1a7241```](https://github.com/ktmeaton/plague-phylogeography/commit/5e1a7241) RAEDNE EAGER setup
+* [```4784bd3f```](https://github.com/ktmeaton/plague-phylogeography/commit/4784bd3f) eager tsv input instructions
+* [```3bb30747```](https://github.com/ktmeaton/plague-phylogeography/commit/3bb30747) change mask char to X!
+* [```a4ce2754```](https://github.com/ktmeaton/plague-phylogeography/commit/a4ce2754) Notes about adding more repeat masking
+* [```1e27c3c7```](https://github.com/ktmeaton/plague-phylogeography/commit/1e27c3c7) being sra for download
+* [```63ac9e0c```](https://github.com/ktmeaton/plague-phylogeography/commit/63ac9e0c) test bronze age sra select
+* [```72831bed```](https://github.com/ktmeaton/plague-phylogeography/commit/72831bed) test sra sqlite select
+* [```63b6e597```](https://github.com/ktmeaton/plague-phylogeography/commit/63b6e597) add Rise of the Bronze Age project to BioSample search
+* [```44d54fe0```](https://github.com/ktmeaton/plague-phylogeography/commit/44d54fe0) remove modeltest-ng from dependencies
+* [```62dce50e```](https://github.com/ktmeaton/plague-phylogeography/commit/62dce50e) new db after pairwise aln filter
+* [```41ae09ea```](https://github.com/ktmeaton/plague-phylogeography/commit/41ae09ea) drop master join tables before new join
+* [```affb1c0d```](https://github.com/ktmeaton/plague-phylogeography/commit/affb1c0d) doc modelfinder changes
+* [```1e4897a6```](https://github.com/ktmeaton/plague-phylogeography/commit/1e4897a6) pairwise align filter
+* [```87710335```](https://github.com/ktmeaton/plague-phylogeography/commit/87710335) remove modeltest-ng use modelfinder instead
+* [```e9d7d8d2```](https://github.com/ktmeaton/plague-phylogeography/commit/e9d7d8d2) fix compare repo and commits
 
 ## v0.1.0
 
 ### Commits
 
-* [```7001e16```](https://github.com/ktmeaton/plague-phylogeography/commit/7001e16) last wrap up before v0.1.0
-* [```0f7d3e4```](https://github.com/ktmeaton/plague-phylogeography/commit/0f7d3e4) fix outdir to always include baseDir
-* [```731888f```](https://github.com/ktmeaton/plague-phylogeography/commit/731888f) add the baseDir prefix to outdir path
-* [```9ffdf65```](https://github.com/ktmeaton/plague-phylogeography/commit/9ffdf65) remove dummy io and workflow name file names
-* [```9268224```](https://github.com/ktmeaton/plague-phylogeography/commit/9268224) introduce dummy io
-* [```4994cf8```](https://github.com/ktmeaton/plague-phylogeography/commit/4994cf8) fix outgroup to Reference
-* [```883ae5d```](https://github.com/ktmeaton/plague-phylogeography/commit/883ae5d) remove hardcode filter5 in iqtree
-* [```23e1e4c```](https://github.com/ktmeaton/plague-phylogeography/commit/23e1e4c) Add iqtree to env dependency
-* [```d1d86ec```](https://github.com/ktmeaton/plague-phylogeography/commit/d1d86ec) make default no missing data
-* [```0ef7ad9```](https://github.com/ktmeaton/plague-phylogeography/commit/0ef7ad9) restore multiple alignment filtering
-* [```3514bf2```](https://github.com/ktmeaton/plague-phylogeography/commit/3514bf2) select forced overwriting
-* [```0533f30```](https://github.com/ktmeaton/plague-phylogeography/commit/0533f30) update default resources and trace param
-* [```e377957```](https://github.com/ktmeaton/plague-phylogeography/commit/e377957) add new corrected ncbimeta db
-* [```4e66741```](https://github.com/ktmeaton/plague-phylogeography/commit/4e66741) clarify snpeff config edit
-* [```65894b2```](https://github.com/ktmeaton/plague-phylogeography/commit/65894b2) remove debugging echo
-* [```df282ab```](https://github.com/ktmeaton/plague-phylogeography/commit/df282ab) simplify assembly ftp parsing
-* [```d2a4606```](https://github.com/ktmeaton/plague-phylogeography/commit/d2a4606) add a third join to fix ambiguous ftp
-* [```a14e1e4```](https://github.com/ktmeaton/plague-phylogeography/commit/a14e1e4) new scripts and phylo methods
-* [```5240049```](https://github.com/ktmeaton/plague-phylogeography/commit/5240049) remove the commands
-* [```ec2b8e5```](https://github.com/ktmeaton/plague-phylogeography/commit/ec2b8e5) add new sql select on AssemblyFTPGenbank
-* [```73008d1```](https://github.com/ktmeaton/plague-phylogeography/commit/73008d1) complete sql command
-* [```623152c```](https://github.com/ktmeaton/plague-phylogeography/commit/623152c) nextflow typo fix
-* [```73944c8```](https://github.com/ktmeaton/plague-phylogeography/commit/73944c8) add nextflow dependency
-* [```82f01da```](https://github.com/ktmeaton/plague-phylogeography/commit/82f01da) remove join commands
-* [```9acb077```](https://github.com/ktmeaton/plague-phylogeography/commit/9acb077) closing parentheses
-* [```f2ab41a```](https://github.com/ktmeaton/plague-phylogeography/commit/f2ab41a) sql line 6
-* [```22a1239```](https://github.com/ktmeaton/plague-phylogeography/commit/22a1239) sql cmd 5 lines
-* [```4cd95fa```](https://github.com/ktmeaton/plague-phylogeography/commit/4cd95fa) wc and sql line 2
-* [```c076fb9```](https://github.com/ktmeaton/plague-phylogeography/commit/c076fb9) update sqlite cmd line 1
-* [```383b6d5```](https://github.com/ktmeaton/plague-phylogeography/commit/383b6d5) change iqtree cpus from auto to nf task cpus
-* [```d3c7f20```](https://github.com/ktmeaton/plague-phylogeography/commit/d3c7f20) fix config and nf var
-* [```e3ed3b1```](https://github.com/ktmeaton/plague-phylogeography/commit/e3ed3b1) iqtree test
-* [```7925ad3```](https://github.com/ktmeaton/plague-phylogeography/commit/7925ad3) new skip commands and new sql command
-* [```81d996c```](https://github.com/ktmeaton/plague-phylogeography/commit/81d996c) topology is unknown parameter
-* [```bc136ce```](https://github.com/ktmeaton/plague-phylogeography/commit/bc136ce) remove slow filter section JUST FOR TEST
-* [```9c7fb74```](https://github.com/ktmeaton/plague-phylogeography/commit/9c7fb74) demo ml phylogeny method
-* [```eefbe8f```](https://github.com/ktmeaton/plague-phylogeography/commit/eefbe8f) demo modeltest run
-* [```86c30ef```](https://github.com/ktmeaton/plague-phylogeography/commit/86c30ef) allow modeltest echo
-* [```b40d913```](https://github.com/ktmeaton/plague-phylogeography/commit/b40d913) new SQL command for testing
-* [```90ae1b2```](https://github.com/ktmeaton/plague-phylogeography/commit/90ae1b2) fix snpeff snippy csv channel output
-* [```50d4553```](https://github.com/ktmeaton/plague-phylogeography/commit/50d4553) fix char escape error
-* [```d97a91b```](https://github.com/ktmeaton/plague-phylogeography/commit/d97a91b) rename default snippy csv
-* [```e3732a5```](https://github.com/ktmeaton/plague-phylogeography/commit/e3732a5) specify correct path
-* [```3dbe516```](https://github.com/ktmeaton/plague-phylogeography/commit/3dbe516) snpeff stats fix
-* [```3ad35ed```](https://github.com/ktmeaton/plague-phylogeography/commit/3ad35ed) add snpeff db name
-* [```ba930f7```](https://github.com/ktmeaton/plague-phylogeography/commit/ba930f7) add snpeff stats
-* [```f0705ac```](https://github.com/ktmeaton/plague-phylogeography/commit/f0705ac) snpEff build database
-* [```3c76889```](https://github.com/ktmeaton/plague-phylogeography/commit/3c76889) filter snippy multi
-* [```d9388f3```](https://github.com/ktmeaton/plague-phylogeography/commit/d9388f3) fix fna and gb discrepancy
-* [```f974be2```](https://github.com/ktmeaton/plague-phylogeography/commit/f974be2) merge the master mask bed
-* [```427b10e```](https://github.com/ktmeaton/plague-phylogeography/commit/427b10e) add ftp download of reference gb
-* [```eba7679```](https://github.com/ktmeaton/plague-phylogeography/commit/eba7679) start adding resource constraints
-* [```326ae1e```](https://github.com/ktmeaton/plague-phylogeography/commit/326ae1e) reorganize as full and partial
-* [```c9bf157```](https://github.com/ktmeaton/plague-phylogeography/commit/c9bf157) add updated db for testing
-* [```00bdc22```](https://github.com/ktmeaton/plague-phylogeography/commit/00bdc22) large update notation
-* [```6c4ac9c```](https://github.com/ktmeaton/plague-phylogeography/commit/6c4ac9c) include stats link in docs
-* [```64948a5```](https://github.com/ktmeaton/plague-phylogeography/commit/64948a5) new pipeline flowchart image
-* [```ce1291f```](https://github.com/ktmeaton/plague-phylogeography/commit/ce1291f) multiqc docs
-* [```082af7b```](https://github.com/ktmeaton/plague-phylogeography/commit/082af7b) fix minor typo
-* [```8a775ee```](https://github.com/ktmeaton/plague-phylogeography/commit/8a775ee) correct params namespace
-* [```14c42b1```](https://github.com/ktmeaton/plague-phylogeography/commit/14c42b1) multiqc and qualimap
-* [```3f0caa1```](https://github.com/ktmeaton/plague-phylogeography/commit/3f0caa1) qualimap stats docs
-* [```8642a6b```](https://github.com/ktmeaton/plague-phylogeography/commit/8642a6b) multiqc config file
-* [```283adc5```](https://github.com/ktmeaton/plague-phylogeography/commit/283adc5) remove extra annot files
-* [```012957b```](https://github.com/ktmeaton/plague-phylogeography/commit/012957b) add bam file to channel doc
-* [```0e92aa0```](https://github.com/ktmeaton/plague-phylogeography/commit/0e92aa0) add multiqc dependency
-* [```cb3558c```](https://github.com/ktmeaton/plague-phylogeography/commit/cb3558c) add qualimap to dependencies
-* [```b5c51aa```](https://github.com/ktmeaton/plague-phylogeography/commit/b5c51aa) ignore any results like folder
-* [```49ed3b3```](https://github.com/ktmeaton/plague-phylogeography/commit/49ed3b3) full pipeline command
-* [```7201b71```](https://github.com/ktmeaton/plague-phylogeography/commit/7201b71) latest trace files
-* [```00c33aa```](https://github.com/ktmeaton/plague-phylogeography/commit/00c33aa) remove echo true statements
-* [```c855c0f```](https://github.com/ktmeaton/plague-phylogeography/commit/c855c0f) restore pipeline0 as main pipeline
-* [```3338f7f```](https://github.com/ktmeaton/plague-phylogeography/commit/3338f7f) working snp high density
-* [```0d552d8```](https://github.com/ktmeaton/plague-phylogeography/commit/0d552d8) docs for snippy high density
-* [```97be4b6```](https://github.com/ktmeaton/plague-phylogeography/commit/97be4b6) fix underline and remove modindex
-* [```15f9d68```](https://github.com/ktmeaton/plague-phylogeography/commit/15f9d68) fix publish and save before trying mix
-* [```b00e47b```](https://github.com/ktmeaton/plague-phylogeography/commit/b00e47b) more explit typing
-* [```aafcb18```](https://github.com/ktmeaton/plague-phylogeography/commit/aafcb18) snippy var summary docs
-* [```29f5421```](https://github.com/ktmeaton/plague-phylogeography/commit/29f5421) snippy var summary doc
-* [```26bf56f```](https://github.com/ktmeaton/plague-phylogeography/commit/26bf56f) snippy pairwise docs
-* [```aa5204e```](https://github.com/ktmeaton/plague-phylogeography/commit/aa5204e) snippy pairwise docs
-* [```7109c88```](https://github.com/ktmeaton/plague-phylogeography/commit/7109c88) assembly download
-* [```8ccf7d6```](https://github.com/ktmeaton/plague-phylogeography/commit/8ccf7d6) assembly download sorted
-* [```d2e247f```](https://github.com/ktmeaton/plague-phylogeography/commit/d2e247f) assembly download ch reorganize
-* [```317e32f```](https://github.com/ktmeaton/plague-phylogeography/commit/317e32f) formatting and process specs
-* [```f6f9e91```](https://github.com/ktmeaton/plague-phylogeography/commit/f6f9e91) data download docs
-* [```3ead1e4```](https://github.com/ktmeaton/plague-phylogeography/commit/3ead1e4) add ncbimeta_annot default false
-* [```2e76366```](https://github.com/ktmeaton/plague-phylogeography/commit/2e76366) tested sqlite import
-* [```9149afb```](https://github.com/ktmeaton/plague-phylogeography/commit/9149afb) sqlite import
-* [```94dcb58```](https://github.com/ktmeaton/plague-phylogeography/commit/94dcb58) new join method
-* [```d214ed2```](https://github.com/ktmeaton/plague-phylogeography/commit/d214ed2) add ncbimeta create and update docs
-* [```ee6ca6b```](https://github.com/ktmeaton/plague-phylogeography/commit/ee6ca6b) fix headers and ftp input name
-* [```1f48a3b```](https://github.com/ktmeaton/plague-phylogeography/commit/1f48a3b) use a process link file to organize
-* [```a6dcf38```](https://github.com/ktmeaton/plague-phylogeography/commit/a6dcf38) create and update db
-* [```411c886```](https://github.com/ktmeaton/plague-phylogeography/commit/411c886) more publish docs for repeats and low-complexity
-* [```c11a9d2```](https://github.com/ktmeaton/plague-phylogeography/commit/c11a9d2) detect repeats and low-complexity
-* [```03e5eda```](https://github.com/ktmeaton/plague-phylogeography/commit/03e5eda) ref download docs
-* [```05d5c68```](https://github.com/ktmeaton/plague-phylogeography/commit/05d5c68) remove unneccesary complete flags
-* [```3a292c1```](https://github.com/ktmeaton/plague-phylogeography/commit/3a292c1) add publish info to docstring
-* [```d0fc809```](https://github.com/ktmeaton/plague-phylogeography/commit/d0fc809) new annot file for biosample
-* [```3fc83b2```](https://github.com/ktmeaton/plague-phylogeography/commit/3fc83b2) burn down build up with nice doc
-* [```b2352b5```](https://github.com/ktmeaton/plague-phylogeography/commit/b2352b5) move config param to sep file
-* [```63194dd```](https://github.com/ktmeaton/plague-phylogeography/commit/63194dd) fix update example command
-* [```64330ad```](https://github.com/ktmeaton/plague-phylogeography/commit/64330ad) add paper sphinx and background text
-* [```064cc97```](https://github.com/ktmeaton/plague-phylogeography/commit/064cc97) ReadTheDocs init
-* [```8162678```](https://github.com/ktmeaton/plague-phylogeography/commit/8162678) ncbimeta.yaml file specific
-* [```2baebbc```](https://github.com/ktmeaton/plague-phylogeography/commit/2baebbc) rearrange pipeline fig
-* [```4ee7107```](https://github.com/ktmeaton/plague-phylogeography/commit/4ee7107) some dev sphinx dependencies
-* [```b061577```](https://github.com/ktmeaton/plague-phylogeography/commit/b061577) only execute pipeline if db has been updated or sqlite input specified
-* [```08738a9```](https://github.com/ktmeaton/plague-phylogeography/commit/08738a9) add config back to worktree
-* [```bc5a6d9```](https://github.com/ktmeaton/plague-phylogeography/commit/bc5a6d9) formatting fix
-* [```dfad8c4```](https://github.com/ktmeaton/plague-phylogeography/commit/dfad8c4) update ncbimeta config to v0.6.5 [clear]
-* [```b36512b```](https://github.com/ktmeaton/plague-phylogeography/commit/b36512b) update ncbimeta dependency to v0.6.5
-* [```3a1946b```](https://github.com/ktmeaton/plague-phylogeography/commit/3a1946b) change extract file to annot_biosample
-* [```f7205da```](https://github.com/ktmeaton/plague-phylogeography/commit/f7205da) snp high density filtering
-* [```6c9d877```](https://github.com/ktmeaton/plague-phylogeography/commit/6c9d877) add requirement vcftools
-* [```f762f62```](https://github.com/ktmeaton/plague-phylogeography/commit/f762f62) tested process reference_detect_repeats
-* [```27178fc```](https://github.com/ktmeaton/plague-phylogeography/commit/27178fc) add modeltest-ng to requirements
-* [```5e6ace1```](https://github.com/ktmeaton/plague-phylogeography/commit/5e6ace1) prototype repeat detection
-* [```4d1a4d5```](https://github.com/ktmeaton/plague-phylogeography/commit/4d1a4d5) add modeltest-ng to env
-* [```2f1b97d```](https://github.com/ktmeaton/plague-phylogeography/commit/2f1b97d) readd yaml
-* [```1ddbda9```](https://github.com/ktmeaton/plague-phylogeography/commit/1ddbda9) retrieve yaml from stash
-* [```25289da```](https://github.com/ktmeaton/plague-phylogeography/commit/25289da) ignore ncbimeta.yaml changes using skip-worktree
-* [```689ded8```](https://github.com/ktmeaton/plague-phylogeography/commit/689ded8) stop tracking file by removing cached info
-* [```9d6beb6```](https://github.com/ktmeaton/plague-phylogeography/commit/9d6beb6) more purge wrangling
-* [```a94a5f1```](https://github.com/ktmeaton/plague-phylogeography/commit/a94a5f1) extra data purge instructions
-* [```a8a2486```](https://github.com/ktmeaton/plague-phylogeography/commit/a8a2486) merge onto info113 after yaml cleanup
-* [```cf752f0```](https://github.com/ktmeaton/plague-phylogeography/commit/cf752f0) ignore all versions of ncbimeta.yaml
-* [```04c0d30```](https://github.com/ktmeaton/plague-phylogeography/commit/04c0d30) copy yaml outside repo dir
-* [```f79635e```](https://github.com/ktmeaton/plague-phylogeography/commit/f79635e) sensitive data deletion
-* [```5dc2519```](https://github.com/ktmeaton/plague-phylogeography/commit/5dc2519) ignore src dir from pip
-* [```926f817```](https://github.com/ktmeaton/plague-phylogeography/commit/926f817) improved join master
-* [```22e4e12```](https://github.com/ktmeaton/plague-phylogeography/commit/22e4e12) join notes
-* [```93fd124```](https://github.com/ktmeaton/plague-phylogeography/commit/93fd124) bioperl typo
-* [```142dc2f```](https://github.com/ktmeaton/plague-phylogeography/commit/142dc2f) sepcify bio perl dependency
-* [```a3f1fc0```](https://github.com/ktmeaton/plague-phylogeography/commit/a3f1fc0) db directory date and workflow name
-* [```a329894```](https://github.com/ktmeaton/plague-phylogeography/commit/a329894) max datasets and formatting
-* [```8cbb83c```](https://github.com/ktmeaton/plague-phylogeography/commit/8cbb83c) install ncbimeta from dev branch for now
-* [```9fdef99```](https://github.com/ktmeaton/plague-phylogeography/commit/9fdef99) refine ncbimeta join calls
-* [```db8d3b0```](https://github.com/ktmeaton/plague-phylogeography/commit/db8d3b0) more general ignore
-* [```d980c91```](https://github.com/ktmeaton/plague-phylogeography/commit/d980c91) add annot param to full pipeline run
-* [```4dcc554```](https://github.com/ktmeaton/plague-phylogeography/commit/4dcc554) pipeline flow chart
-* [```a9c99a0```](https://github.com/ktmeaton/plague-phylogeography/commit/a9c99a0) as convert into
-* [```8a0cc47```](https://github.com/ktmeaton/plague-phylogeography/commit/8a0cc47) uniq channel names
-* [```1930b37```](https://github.com/ktmeaton/plague-phylogeography/commit/1930b37) param checking for ncbimeta update channels
-* [```1b950c7```](https://github.com/ktmeaton/plague-phylogeography/commit/1b950c7) trace line endings
-* [```738f1d7```](https://github.com/ktmeaton/plague-phylogeography/commit/738f1d7) format header
-* [```9fafefc```](https://github.com/ktmeaton/plague-phylogeography/commit/9fafefc) ignore trace files
-* [```8e6c98e```](https://github.com/ktmeaton/plague-phylogeography/commit/8e6c98e) full pipeline and trace info
-* [```0d2910c```](https://github.com/ktmeaton/plague-phylogeography/commit/0d2910c) filter empty lines in sql import
-* [```620b5bf```](https://github.com/ktmeaton/plague-phylogeography/commit/620b5bf) Merge from server and local, runname and join conflict
-* [```1fd62d0```](https://github.com/ktmeaton/plague-phylogeography/commit/1fd62d0) runName from date naming
-* [```53fb21d```](https://github.com/ktmeaton/plague-phylogeography/commit/53fb21d) Add second ncbimeta join
-* [```2dbcfa9```](https://github.com/ktmeaton/plague-phylogeography/commit/2dbcfa9) change database directory naming from date to runName
-* [```a88305a```](https://github.com/ktmeaton/plague-phylogeography/commit/a88305a) sql statement avoid REMOVE
-* [```69e460a```](https://github.com/ktmeaton/plague-phylogeography/commit/69e460a) update ncbimeta req to v0.6.4
-* [```cb48e52```](https://github.com/ktmeaton/plague-phylogeography/commit/cb48e52) new annot file prep method
-* [```efd06a5```](https://github.com/ktmeaton/plague-phylogeography/commit/efd06a5) categorize dependencies
-* [```7d61545```](https://github.com/ktmeaton/plague-phylogeography/commit/7d61545) conda env instructions
-* [```29d3f8f```](https://github.com/ktmeaton/plague-phylogeography/commit/29d3f8f) remove test pipeline
-* [```716de11```](https://github.com/ktmeaton/plague-phylogeography/commit/716de11) remove old NCBImeta folder
-* [```e565134```](https://github.com/ktmeaton/plague-phylogeography/commit/e565134) doc filter-branch
-* [```bc32a0e```](https://github.com/ktmeaton/plague-phylogeography/commit/bc32a0e) add ncbimeta.yaml to gitignore
-* [```481f33d```](https://github.com/ktmeaton/plague-phylogeography/commit/481f33d) run from db instructions
-* [```120d7c3```](https://github.com/ktmeaton/plague-phylogeography/commit/120d7c3) annotation and join
-* [```ca830b0```](https://github.com/ktmeaton/plague-phylogeography/commit/ca830b0) remove unnecessary print in variant summary
-* [```b3eee19```](https://github.com/ktmeaton/plague-phylogeography/commit/b3eee19) up to snippy variant summary
-* [```9e98444```](https://github.com/ktmeaton/plague-phylogeography/commit/9e98444) pipeline through but no multi for snippy
-* [```7c19d58```](https://github.com/ktmeaton/plague-phylogeography/commit/7c19d58) good updating dir scheme for now
-* [```12c9b67```](https://github.com/ktmeaton/plague-phylogeography/commit/12c9b67) function ncbimeta
-* [```cb8ab8b```](https://github.com/ktmeaton/plague-phylogeography/commit/cb8ab8b) some update success
-* [```c8088f1```](https://github.com/ktmeaton/plague-phylogeography/commit/c8088f1) db updating
-* [```82d0e33```](https://github.com/ktmeaton/plague-phylogeography/commit/82d0e33) ncbimeta works
-* [```b4c3b8e```](https://github.com/ktmeaton/plague-phylogeography/commit/b4c3b8e) NCBImeta testing
-* [```606fb14```](https://github.com/ktmeaton/plague-phylogeography/commit/606fb14) steps in changelog
-* [```eb2f903```](https://github.com/ktmeaton/plague-phylogeography/commit/eb2f903) tag fix and pairwise
-* [```629a46a```](https://github.com/ktmeaton/plague-phylogeography/commit/629a46a) basedir whitespace struggle
-* [```c9917c0```](https://github.com/ktmeaton/plague-phylogeography/commit/c9917c0) remove conda env force
-* [```8742a57```](https://github.com/ktmeaton/plague-phylogeography/commit/8742a57) sweep update
-* [```fc320bf```](https://github.com/ktmeaton/plague-phylogeography/commit/fc320bf) conda update
-* [```d353b99```](https://github.com/ktmeaton/plague-phylogeography/commit/d353b99) Added CHANGELOG
-* [```15c5aff```](https://github.com/ktmeaton/plague-phylogeography/commit/15c5aff) dustmasker start
-* [```6d5e1a7```](https://github.com/ktmeaton/plague-phylogeography/commit/6d5e1a7) accessory scripts for dustmasker
-* [```264af84```](https://github.com/ktmeaton/plague-phylogeography/commit/264af84) snippy pairwise finish
-* [```71dae42```](https://github.com/ktmeaton/plague-phylogeography/commit/71dae42) dependencies
-* [```9349752```](https://github.com/ktmeaton/plague-phylogeography/commit/9349752) begin snippy
-* [```d49abe5```](https://github.com/ktmeaton/plague-phylogeography/commit/d49abe5) channel config for ftp
-* [```e087cdd```](https://github.com/ktmeaton/plague-phylogeography/commit/e087cdd) commit before channel exp
-* [```38f2a0c```](https://github.com/ktmeaton/plague-phylogeography/commit/38f2a0c) sqlite FTP import success
-* [```911c585```](https://github.com/ktmeaton/plague-phylogeography/commit/911c585) semicolon correct combo
-* [```ecf654b```](https://github.com/ktmeaton/plague-phylogeography/commit/ecf654b) sqlite3 commands
-* [```3c52194```](https://github.com/ktmeaton/plague-phylogeography/commit/3c52194) sqlite file load
-* [```526d325```](https://github.com/ktmeaton/plague-phylogeography/commit/526d325) remove nf-core header
-* [```82ebdbe```](https://github.com/ktmeaton/plague-phylogeography/commit/82ebdbe) before nf-core header remove
-* [```74c9a3d```](https://github.com/ktmeaton/plague-phylogeography/commit/74c9a3d) colored header help start
-* [```4bdc7b9```](https://github.com/ktmeaton/plague-phylogeography/commit/4bdc7b9) minor edit
-* [```833de34```](https://github.com/ktmeaton/plague-phylogeography/commit/833de34) init pipeline
-* [```e881005```](https://github.com/ktmeaton/plague-phylogeography/commit/e881005) Nucleotide annotation fix update
-* [```fc7b7f9```](https://github.com/ktmeaton/plague-phylogeography/commit/fc7b7f9) annotation files update
-* [```e067477```](https://github.com/ktmeaton/plague-phylogeography/commit/e067477) Add Justinian strain rename part 1
-* [```390dd22```](https://github.com/ktmeaton/plague-phylogeography/commit/390dd22) Remove quotations
-* [```8d2f6bf```](https://github.com/ktmeaton/plague-phylogeography/commit/8d2f6bf) Database update, REMOVE annot
-* [```8d06ea1```](https://github.com/ktmeaton/plague-phylogeography/commit/8d06ea1) db cleanup
-* [```3dd2ac1```](https://github.com/ktmeaton/plague-phylogeography/commit/3dd2ac1) Clarify organization parsing
-* [```93b7a82```](https://github.com/ktmeaton/plague-phylogeography/commit/93b7a82) save before move
-* [```9ca9c83```](https://github.com/ktmeaton/plague-phylogeography/commit/9ca9c83) Clean previous db
-* [```0e93fce```](https://github.com/ktmeaton/plague-phylogeography/commit/0e93fce) Update README.md
-* [```8badbae```](https://github.com/ktmeaton/plague-phylogeography/commit/8badbae) First completion of master join table
-* [```3586b7a```](https://github.com/ktmeaton/plague-phylogeography/commit/3586b7a) Sanity commit before database redo
-* [```4cc04a7```](https://github.com/ktmeaton/plague-phylogeography/commit/4cc04a7) Prepared for Join
-* [```395e705```](https://github.com/ktmeaton/plague-phylogeography/commit/395e705) Ongoing db filtering
-* [```b22b367```](https://github.com/ktmeaton/plague-phylogeography/commit/b22b367) Begin database construction
-* [```c1fa844```](https://github.com/ktmeaton/plague-phylogeography/commit/c1fa844) Forgot to add README
-* [```bea5cd5```](https://github.com/ktmeaton/plague-phylogeography/commit/bea5cd5) Database created
-* [```dd20240```](https://github.com/ktmeaton/plague-phylogeography/commit/dd20240) Code reformat
-* [```1e7ff9c```](https://github.com/ktmeaton/plague-phylogeography/commit/1e7ff9c) Data acquisition doc
-* [```82eed2a```](https://github.com/ktmeaton/plague-phylogeography/commit/82eed2a) Update README.md
+* [```7001e16c```](https://github.com/ktmeaton/plague-phylogeography/commit/7001e16c) last wrap up before v0.1.0
+* [```0f7d3e4c```](https://github.com/ktmeaton/plague-phylogeography/commit/0f7d3e4c) fix outdir to always include baseDir
+* [```731888f2```](https://github.com/ktmeaton/plague-phylogeography/commit/731888f2) add the baseDir prefix to outdir path
+* [```9ffdf658```](https://github.com/ktmeaton/plague-phylogeography/commit/9ffdf658) remove dummy io and workflow name file names
+* [```9268224d```](https://github.com/ktmeaton/plague-phylogeography/commit/9268224d) introduce dummy io
+* [```4994cf81```](https://github.com/ktmeaton/plague-phylogeography/commit/4994cf81) fix outgroup to Reference
+* [```883ae5d7```](https://github.com/ktmeaton/plague-phylogeography/commit/883ae5d7) remove hardcode filter5 in iqtree
+* [```23e1e4ce```](https://github.com/ktmeaton/plague-phylogeography/commit/23e1e4ce) Add iqtree to env dependency
+* [```d1d86ec7```](https://github.com/ktmeaton/plague-phylogeography/commit/d1d86ec7) make default no missing data
+* [```0ef7ad99```](https://github.com/ktmeaton/plague-phylogeography/commit/0ef7ad99) restore multiple alignment filtering
+* [```3514bf29```](https://github.com/ktmeaton/plague-phylogeography/commit/3514bf29) select forced overwriting
+* [```0533f308```](https://github.com/ktmeaton/plague-phylogeography/commit/0533f308) update default resources and trace param
+* [```e3779574```](https://github.com/ktmeaton/plague-phylogeography/commit/e3779574) add new corrected ncbimeta db
+* [```4e66741f```](https://github.com/ktmeaton/plague-phylogeography/commit/4e66741f) clarify snpeff config edit
+* [```65894b21```](https://github.com/ktmeaton/plague-phylogeography/commit/65894b21) remove debugging echo
+* [```df282abd```](https://github.com/ktmeaton/plague-phylogeography/commit/df282abd) simplify assembly ftp parsing
+* [```d2a46069```](https://github.com/ktmeaton/plague-phylogeography/commit/d2a46069) add a third join to fix ambiguous ftp
+* [```a14e1e44```](https://github.com/ktmeaton/plague-phylogeography/commit/a14e1e44) new scripts and phylo methods
+* [```52400492```](https://github.com/ktmeaton/plague-phylogeography/commit/52400492) remove the commands
+* [```ec2b8e54```](https://github.com/ktmeaton/plague-phylogeography/commit/ec2b8e54) add new sql select on AssemblyFTPGenbank
+* [```73008d1f```](https://github.com/ktmeaton/plague-phylogeography/commit/73008d1f) complete sql command
+* [```623152c7```](https://github.com/ktmeaton/plague-phylogeography/commit/623152c7) nextflow typo fix
+* [```73944c80```](https://github.com/ktmeaton/plague-phylogeography/commit/73944c80) add nextflow dependency
+* [```82f01dae```](https://github.com/ktmeaton/plague-phylogeography/commit/82f01dae) remove join commands
+* [```9acb0771```](https://github.com/ktmeaton/plague-phylogeography/commit/9acb0771) closing parentheses
+* [```f2ab41a9```](https://github.com/ktmeaton/plague-phylogeography/commit/f2ab41a9) sql line 6
+* [```22a12393```](https://github.com/ktmeaton/plague-phylogeography/commit/22a12393) sql cmd 5 lines
+* [```4cd95fa9```](https://github.com/ktmeaton/plague-phylogeography/commit/4cd95fa9) wc and sql line 2
+* [```c076fb92```](https://github.com/ktmeaton/plague-phylogeography/commit/c076fb92) update sqlite cmd line 1
+* [```383b6d58```](https://github.com/ktmeaton/plague-phylogeography/commit/383b6d58) change iqtree cpus from auto to nf task cpus
+* [```d3c7f20f```](https://github.com/ktmeaton/plague-phylogeography/commit/d3c7f20f) fix config and nf var
+* [```e3ed3b13```](https://github.com/ktmeaton/plague-phylogeography/commit/e3ed3b13) iqtree test
+* [```7925ad3e```](https://github.com/ktmeaton/plague-phylogeography/commit/7925ad3e) new skip commands and new sql command
+* [```81d996c0```](https://github.com/ktmeaton/plague-phylogeography/commit/81d996c0) topology is unknown parameter
+* [```bc136ce8```](https://github.com/ktmeaton/plague-phylogeography/commit/bc136ce8) remove slow filter section JUST FOR TEST
+* [```9c7fb742```](https://github.com/ktmeaton/plague-phylogeography/commit/9c7fb742) demo ml phylogeny method
+* [```eefbe8fe```](https://github.com/ktmeaton/plague-phylogeography/commit/eefbe8fe) demo modeltest run
+* [```86c30ef5```](https://github.com/ktmeaton/plague-phylogeography/commit/86c30ef5) allow modeltest echo
+* [```b40d9137```](https://github.com/ktmeaton/plague-phylogeography/commit/b40d9137) new SQL command for testing
+* [```90ae1b2d```](https://github.com/ktmeaton/plague-phylogeography/commit/90ae1b2d) fix snpeff snippy csv channel output
+* [```50d45533```](https://github.com/ktmeaton/plague-phylogeography/commit/50d45533) fix char escape error
+* [```d97a91b2```](https://github.com/ktmeaton/plague-phylogeography/commit/d97a91b2) rename default snippy csv
+* [```e3732a53```](https://github.com/ktmeaton/plague-phylogeography/commit/e3732a53) specify correct path
+* [```3dbe5162```](https://github.com/ktmeaton/plague-phylogeography/commit/3dbe5162) snpeff stats fix
+* [```3ad35ed4```](https://github.com/ktmeaton/plague-phylogeography/commit/3ad35ed4) add snpeff db name
+* [```ba930f7c```](https://github.com/ktmeaton/plague-phylogeography/commit/ba930f7c) add snpeff stats
+* [```f0705ac8```](https://github.com/ktmeaton/plague-phylogeography/commit/f0705ac8) snpEff build database
+* [```3c768893```](https://github.com/ktmeaton/plague-phylogeography/commit/3c768893) filter snippy multi
+* [```d9388f33```](https://github.com/ktmeaton/plague-phylogeography/commit/d9388f33) fix fna and gb discrepancy
+* [```f974be2a```](https://github.com/ktmeaton/plague-phylogeography/commit/f974be2a) merge the master mask bed
+* [```427b10e3```](https://github.com/ktmeaton/plague-phylogeography/commit/427b10e3) add ftp download of reference gb
+* [```eba76791```](https://github.com/ktmeaton/plague-phylogeography/commit/eba76791) start adding resource constraints
+* [```326ae1e1```](https://github.com/ktmeaton/plague-phylogeography/commit/326ae1e1) reorganize as full and partial
+* [```c9bf1576```](https://github.com/ktmeaton/plague-phylogeography/commit/c9bf1576) add updated db for testing
+* [```00bdc224```](https://github.com/ktmeaton/plague-phylogeography/commit/00bdc224) large update notation
+* [```6c4ac9c0```](https://github.com/ktmeaton/plague-phylogeography/commit/6c4ac9c0) include stats link in docs
+* [```64948a50```](https://github.com/ktmeaton/plague-phylogeography/commit/64948a50) new pipeline flowchart image
+* [```ce1291fd```](https://github.com/ktmeaton/plague-phylogeography/commit/ce1291fd) multiqc docs
+* [```082af7b2```](https://github.com/ktmeaton/plague-phylogeography/commit/082af7b2) fix minor typo
+* [```8a775ee1```](https://github.com/ktmeaton/plague-phylogeography/commit/8a775ee1) correct params namespace
+* [```14c42b10```](https://github.com/ktmeaton/plague-phylogeography/commit/14c42b10) multiqc and qualimap
+* [```3f0caa12```](https://github.com/ktmeaton/plague-phylogeography/commit/3f0caa12) qualimap stats docs
+* [```8642a6b1```](https://github.com/ktmeaton/plague-phylogeography/commit/8642a6b1) multiqc config file
+* [```283adc5d```](https://github.com/ktmeaton/plague-phylogeography/commit/283adc5d) remove extra annot files
+* [```012957b1```](https://github.com/ktmeaton/plague-phylogeography/commit/012957b1) add bam file to channel doc
+* [```0e92aa0f```](https://github.com/ktmeaton/plague-phylogeography/commit/0e92aa0f) add multiqc dependency
+* [```cb3558c7```](https://github.com/ktmeaton/plague-phylogeography/commit/cb3558c7) add qualimap to dependencies
+* [```b5c51aa1```](https://github.com/ktmeaton/plague-phylogeography/commit/b5c51aa1) ignore any results like folder
+* [```49ed3b31```](https://github.com/ktmeaton/plague-phylogeography/commit/49ed3b31) full pipeline command
+* [```7201b719```](https://github.com/ktmeaton/plague-phylogeography/commit/7201b719) latest trace files
+* [```00c33aa6```](https://github.com/ktmeaton/plague-phylogeography/commit/00c33aa6) remove echo true statements
+* [```c855c0f5```](https://github.com/ktmeaton/plague-phylogeography/commit/c855c0f5) restore pipeline0 as main pipeline
+* [```3338f7f7```](https://github.com/ktmeaton/plague-phylogeography/commit/3338f7f7) working snp high density
+* [```0d552d8a```](https://github.com/ktmeaton/plague-phylogeography/commit/0d552d8a) docs for snippy high density
+* [```97be4b6d```](https://github.com/ktmeaton/plague-phylogeography/commit/97be4b6d) fix underline and remove modindex
+* [```15f9d689```](https://github.com/ktmeaton/plague-phylogeography/commit/15f9d689) fix publish and save before trying mix
+* [```b00e47bd```](https://github.com/ktmeaton/plague-phylogeography/commit/b00e47bd) more explit typing
+* [```aafcb184```](https://github.com/ktmeaton/plague-phylogeography/commit/aafcb184) snippy var summary docs
+* [```29f5421f```](https://github.com/ktmeaton/plague-phylogeography/commit/29f5421f) snippy var summary doc
+* [```26bf56f7```](https://github.com/ktmeaton/plague-phylogeography/commit/26bf56f7) snippy pairwise docs
+* [```aa5204e7```](https://github.com/ktmeaton/plague-phylogeography/commit/aa5204e7) snippy pairwise docs
+* [```7109c886```](https://github.com/ktmeaton/plague-phylogeography/commit/7109c886) assembly download
+* [```8ccf7d61```](https://github.com/ktmeaton/plague-phylogeography/commit/8ccf7d61) assembly download sorted
+* [```d2e247f6```](https://github.com/ktmeaton/plague-phylogeography/commit/d2e247f6) assembly download ch reorganize
+* [```317e32f6```](https://github.com/ktmeaton/plague-phylogeography/commit/317e32f6) formatting and process specs
+* [```f6f9e910```](https://github.com/ktmeaton/plague-phylogeography/commit/f6f9e910) data download docs
+* [```3ead1e46```](https://github.com/ktmeaton/plague-phylogeography/commit/3ead1e46) add ncbimeta_annot default false
+* [```2e76366c```](https://github.com/ktmeaton/plague-phylogeography/commit/2e76366c) tested sqlite import
+* [```9149afb5```](https://github.com/ktmeaton/plague-phylogeography/commit/9149afb5) sqlite import
+* [```94dcb58a```](https://github.com/ktmeaton/plague-phylogeography/commit/94dcb58a) new join method
+* [```d214ed2f```](https://github.com/ktmeaton/plague-phylogeography/commit/d214ed2f) add ncbimeta create and update docs
+* [```ee6ca6b2```](https://github.com/ktmeaton/plague-phylogeography/commit/ee6ca6b2) fix headers and ftp input name
+* [```1f48a3bf```](https://github.com/ktmeaton/plague-phylogeography/commit/1f48a3bf) use a process link file to organize
+* [```a6dcf387```](https://github.com/ktmeaton/plague-phylogeography/commit/a6dcf387) create and update db
+* [```411c886c```](https://github.com/ktmeaton/plague-phylogeography/commit/411c886c) more publish docs for repeats and low-complexity
+* [```c11a9d2f```](https://github.com/ktmeaton/plague-phylogeography/commit/c11a9d2f) detect repeats and low-complexity
+* [```03e5eda6```](https://github.com/ktmeaton/plague-phylogeography/commit/03e5eda6) ref download docs
+* [```05d5c681```](https://github.com/ktmeaton/plague-phylogeography/commit/05d5c681) remove unneccesary complete flags
+* [```3a292c1b```](https://github.com/ktmeaton/plague-phylogeography/commit/3a292c1b) add publish info to docstring
+* [```d0fc809b```](https://github.com/ktmeaton/plague-phylogeography/commit/d0fc809b) new annot file for biosample
+* [```3fc83b27```](https://github.com/ktmeaton/plague-phylogeography/commit/3fc83b27) burn down build up with nice doc
+* [```b2352b5b```](https://github.com/ktmeaton/plague-phylogeography/commit/b2352b5b) move config param to sep file
+* [```63194dd3```](https://github.com/ktmeaton/plague-phylogeography/commit/63194dd3) fix update example command
+* [```64330adc```](https://github.com/ktmeaton/plague-phylogeography/commit/64330adc) add paper sphinx and background text
+* [```064cc97b```](https://github.com/ktmeaton/plague-phylogeography/commit/064cc97b) ReadTheDocs init
+* [```81626789```](https://github.com/ktmeaton/plague-phylogeography/commit/81626789) ncbimeta.yaml file specific
+* [```2baebbc5```](https://github.com/ktmeaton/plague-phylogeography/commit/2baebbc5) rearrange pipeline fig
+* [```4ee71078```](https://github.com/ktmeaton/plague-phylogeography/commit/4ee71078) some dev sphinx dependencies
+* [```b0615771```](https://github.com/ktmeaton/plague-phylogeography/commit/b0615771) only execute pipeline if db has been updated or sqlite input specified
+* [```08738a9f```](https://github.com/ktmeaton/plague-phylogeography/commit/08738a9f) add config back to worktree
+* [```bc5a6d9b```](https://github.com/ktmeaton/plague-phylogeography/commit/bc5a6d9b) formatting fix
+* [```dfad8c4e```](https://github.com/ktmeaton/plague-phylogeography/commit/dfad8c4e) update ncbimeta config to v0.6.5 [clear]
+* [```b36512b7```](https://github.com/ktmeaton/plague-phylogeography/commit/b36512b7) update ncbimeta dependency to v0.6.5
+* [```3a1946b6```](https://github.com/ktmeaton/plague-phylogeography/commit/3a1946b6) change extract file to annot_biosample
+* [```f7205dab```](https://github.com/ktmeaton/plague-phylogeography/commit/f7205dab) snp high density filtering
+* [```6c9d8775```](https://github.com/ktmeaton/plague-phylogeography/commit/6c9d8775) add requirement vcftools
+* [```f762f62e```](https://github.com/ktmeaton/plague-phylogeography/commit/f762f62e) tested process reference_detect_repeats
+* [```27178fce```](https://github.com/ktmeaton/plague-phylogeography/commit/27178fce) add modeltest-ng to requirements
+* [```5e6ace1a```](https://github.com/ktmeaton/plague-phylogeography/commit/5e6ace1a) prototype repeat detection
+* [```4d1a4d51```](https://github.com/ktmeaton/plague-phylogeography/commit/4d1a4d51) add modeltest-ng to env
+* [```2f1b97d7```](https://github.com/ktmeaton/plague-phylogeography/commit/2f1b97d7) readd yaml
+* [```1ddbda99```](https://github.com/ktmeaton/plague-phylogeography/commit/1ddbda99) retrieve yaml from stash
+* [```25289da6```](https://github.com/ktmeaton/plague-phylogeography/commit/25289da6) ignore ncbimeta.yaml changes using skip-worktree
+* [```689ded85```](https://github.com/ktmeaton/plague-phylogeography/commit/689ded85) stop tracking file by removing cached info
+* [```9d6beb6f```](https://github.com/ktmeaton/plague-phylogeography/commit/9d6beb6f) more purge wrangling
+* [```a94a5f1d```](https://github.com/ktmeaton/plague-phylogeography/commit/a94a5f1d) extra data purge instructions
+* [```a8a2486f```](https://github.com/ktmeaton/plague-phylogeography/commit/a8a2486f) merge onto info113 after yaml cleanup
+* [```cf752f08```](https://github.com/ktmeaton/plague-phylogeography/commit/cf752f08) ignore all versions of ncbimeta.yaml
+* [```04c0d305```](https://github.com/ktmeaton/plague-phylogeography/commit/04c0d305) copy yaml outside repo dir
+* [```f79635e8```](https://github.com/ktmeaton/plague-phylogeography/commit/f79635e8) sensitive data deletion
+* [```5dc25198```](https://github.com/ktmeaton/plague-phylogeography/commit/5dc25198) ignore src dir from pip
+* [```926f817e```](https://github.com/ktmeaton/plague-phylogeography/commit/926f817e) improved join master
+* [```22e4e121```](https://github.com/ktmeaton/plague-phylogeography/commit/22e4e121) join notes
+* [```93fd1245```](https://github.com/ktmeaton/plague-phylogeography/commit/93fd1245) bioperl typo
+* [```142dc2f7```](https://github.com/ktmeaton/plague-phylogeography/commit/142dc2f7) sepcify bio perl dependency
+* [```a3f1fc0a```](https://github.com/ktmeaton/plague-phylogeography/commit/a3f1fc0a) db directory date and workflow name
+* [```a329894f```](https://github.com/ktmeaton/plague-phylogeography/commit/a329894f) max datasets and formatting
+* [```8cbb83c0```](https://github.com/ktmeaton/plague-phylogeography/commit/8cbb83c0) install ncbimeta from dev branch for now
+* [```9fdef990```](https://github.com/ktmeaton/plague-phylogeography/commit/9fdef990) refine ncbimeta join calls
+* [```db8d3b06```](https://github.com/ktmeaton/plague-phylogeography/commit/db8d3b06) more general ignore
+* [```d980c91a```](https://github.com/ktmeaton/plague-phylogeography/commit/d980c91a) add annot param to full pipeline run
+* [```4dcc554f```](https://github.com/ktmeaton/plague-phylogeography/commit/4dcc554f) pipeline flow chart
+* [```a9c99a0e```](https://github.com/ktmeaton/plague-phylogeography/commit/a9c99a0e) as convert into
+* [```8a0cc47b```](https://github.com/ktmeaton/plague-phylogeography/commit/8a0cc47b) uniq channel names
+* [```1930b379```](https://github.com/ktmeaton/plague-phylogeography/commit/1930b379) param checking for ncbimeta update channels
+* [```1b950c7c```](https://github.com/ktmeaton/plague-phylogeography/commit/1b950c7c) trace line endings
+* [```738f1d7f```](https://github.com/ktmeaton/plague-phylogeography/commit/738f1d7f) format header
+* [```9fafefc6```](https://github.com/ktmeaton/plague-phylogeography/commit/9fafefc6) ignore trace files
+* [```8e6c98e1```](https://github.com/ktmeaton/plague-phylogeography/commit/8e6c98e1) full pipeline and trace info
+* [```0d2910ca```](https://github.com/ktmeaton/plague-phylogeography/commit/0d2910ca) filter empty lines in sql import
+* [```620b5bf7```](https://github.com/ktmeaton/plague-phylogeography/commit/620b5bf7) Merge from server and local, runname and join conflict
+* [```1fd62d00```](https://github.com/ktmeaton/plague-phylogeography/commit/1fd62d00) runName from date naming
+* [```53fb21d1```](https://github.com/ktmeaton/plague-phylogeography/commit/53fb21d1) Add second ncbimeta join
+* [```2dbcfa97```](https://github.com/ktmeaton/plague-phylogeography/commit/2dbcfa97) change database directory naming from date to runName
+* [```a88305ad```](https://github.com/ktmeaton/plague-phylogeography/commit/a88305ad) sql statement avoid REMOVE
+* [```69e460a1```](https://github.com/ktmeaton/plague-phylogeography/commit/69e460a1) update ncbimeta req to v0.6.4
+* [```cb48e524```](https://github.com/ktmeaton/plague-phylogeography/commit/cb48e524) new annot file prep method
+* [```efd06a56```](https://github.com/ktmeaton/plague-phylogeography/commit/efd06a56) categorize dependencies
+* [```7d61545d```](https://github.com/ktmeaton/plague-phylogeography/commit/7d61545d) conda env instructions
+* [```29d3f8f5```](https://github.com/ktmeaton/plague-phylogeography/commit/29d3f8f5) remove test pipeline
+* [```716de11e```](https://github.com/ktmeaton/plague-phylogeography/commit/716de11e) remove old NCBImeta folder
+* [```e5651347```](https://github.com/ktmeaton/plague-phylogeography/commit/e5651347) doc filter-branch
+* [```bc32a0ee```](https://github.com/ktmeaton/plague-phylogeography/commit/bc32a0ee) add ncbimeta.yaml to gitignore
+* [```481f33dc```](https://github.com/ktmeaton/plague-phylogeography/commit/481f33dc) run from db instructions
+* [```120d7c38```](https://github.com/ktmeaton/plague-phylogeography/commit/120d7c38) annotation and join
+* [```ca830b04```](https://github.com/ktmeaton/plague-phylogeography/commit/ca830b04) remove unnecessary print in variant summary
+* [```b3eee191```](https://github.com/ktmeaton/plague-phylogeography/commit/b3eee191) up to snippy variant summary
+* [```9e98444d```](https://github.com/ktmeaton/plague-phylogeography/commit/9e98444d) pipeline through but no multi for snippy
+* [```7c19d588```](https://github.com/ktmeaton/plague-phylogeography/commit/7c19d588) good updating dir scheme for now
+* [```12c9b679```](https://github.com/ktmeaton/plague-phylogeography/commit/12c9b679) function ncbimeta
+* [```cb8ab8b9```](https://github.com/ktmeaton/plague-phylogeography/commit/cb8ab8b9) some update success
+* [```c8088f1c```](https://github.com/ktmeaton/plague-phylogeography/commit/c8088f1c) db updating
+* [```82d0e330```](https://github.com/ktmeaton/plague-phylogeography/commit/82d0e330) ncbimeta works
+* [```b4c3b8e6```](https://github.com/ktmeaton/plague-phylogeography/commit/b4c3b8e6) NCBImeta testing
+* [```606fb14e```](https://github.com/ktmeaton/plague-phylogeography/commit/606fb14e) steps in changelog
+* [```eb2f903c```](https://github.com/ktmeaton/plague-phylogeography/commit/eb2f903c) tag fix and pairwise
+* [```629a46ab```](https://github.com/ktmeaton/plague-phylogeography/commit/629a46ab) basedir whitespace struggle
+* [```c9917c06```](https://github.com/ktmeaton/plague-phylogeography/commit/c9917c06) remove conda env force
+* [```8742a57a```](https://github.com/ktmeaton/plague-phylogeography/commit/8742a57a) sweep update
+* [```fc320bfa```](https://github.com/ktmeaton/plague-phylogeography/commit/fc320bfa) conda update
+* [```d353b99d```](https://github.com/ktmeaton/plague-phylogeography/commit/d353b99d) Added CHANGELOG
+* [```15c5aff9```](https://github.com/ktmeaton/plague-phylogeography/commit/15c5aff9) dustmasker start
+* [```6d5e1a70```](https://github.com/ktmeaton/plague-phylogeography/commit/6d5e1a70) accessory scripts for dustmasker
+* [```264af84d```](https://github.com/ktmeaton/plague-phylogeography/commit/264af84d) snippy pairwise finish
+* [```71dae427```](https://github.com/ktmeaton/plague-phylogeography/commit/71dae427) dependencies
+* [```9349752d```](https://github.com/ktmeaton/plague-phylogeography/commit/9349752d) begin snippy
+* [```d49abe57```](https://github.com/ktmeaton/plague-phylogeography/commit/d49abe57) channel config for ftp
+* [```e087cdda```](https://github.com/ktmeaton/plague-phylogeography/commit/e087cdda) commit before channel exp
+* [```38f2a0cd```](https://github.com/ktmeaton/plague-phylogeography/commit/38f2a0cd) sqlite FTP import success
+* [```911c5855```](https://github.com/ktmeaton/plague-phylogeography/commit/911c5855) semicolon correct combo
+* [```ecf654b2```](https://github.com/ktmeaton/plague-phylogeography/commit/ecf654b2) sqlite3 commands
+* [```3c521948```](https://github.com/ktmeaton/plague-phylogeography/commit/3c521948) sqlite file load
+* [```526d3257```](https://github.com/ktmeaton/plague-phylogeography/commit/526d3257) remove nf-core header
+* [```82ebdbef```](https://github.com/ktmeaton/plague-phylogeography/commit/82ebdbef) before nf-core header remove
+* [```74c9a3dc```](https://github.com/ktmeaton/plague-phylogeography/commit/74c9a3dc) colored header help start
+* [```4bdc7b9b```](https://github.com/ktmeaton/plague-phylogeography/commit/4bdc7b9b) minor edit
+* [```833de349```](https://github.com/ktmeaton/plague-phylogeography/commit/833de349) init pipeline
+* [```e8810054```](https://github.com/ktmeaton/plague-phylogeography/commit/e8810054) Nucleotide annotation fix update
+* [```fc7b7f93```](https://github.com/ktmeaton/plague-phylogeography/commit/fc7b7f93) annotation files update
+* [```e0674773```](https://github.com/ktmeaton/plague-phylogeography/commit/e0674773) Add Justinian strain rename part 1
+* [```390dd220```](https://github.com/ktmeaton/plague-phylogeography/commit/390dd220) Remove quotations
+* [```8d2f6bfa```](https://github.com/ktmeaton/plague-phylogeography/commit/8d2f6bfa) Database update, REMOVE annot
+* [```8d06ea11```](https://github.com/ktmeaton/plague-phylogeography/commit/8d06ea11) db cleanup
+* [```3dd2ac1b```](https://github.com/ktmeaton/plague-phylogeography/commit/3dd2ac1b) Clarify organization parsing
+* [```93b7a822```](https://github.com/ktmeaton/plague-phylogeography/commit/93b7a822) save before move
+* [```9ca9c837```](https://github.com/ktmeaton/plague-phylogeography/commit/9ca9c837) Clean previous db
+* [```0e93fcef```](https://github.com/ktmeaton/plague-phylogeography/commit/0e93fcef) Update README.md
+* [```8badbaea```](https://github.com/ktmeaton/plague-phylogeography/commit/8badbaea) First completion of master join table
+* [```3586b7a8```](https://github.com/ktmeaton/plague-phylogeography/commit/3586b7a8) Sanity commit before database redo
+* [```4cc04a79```](https://github.com/ktmeaton/plague-phylogeography/commit/4cc04a79) Prepared for Join
+* [```395e7051```](https://github.com/ktmeaton/plague-phylogeography/commit/395e7051) Ongoing db filtering
+* [```b22b3676```](https://github.com/ktmeaton/plague-phylogeography/commit/b22b3676) Begin database construction
+* [```c1fa8447```](https://github.com/ktmeaton/plague-phylogeography/commit/c1fa8447) Forgot to add README
+* [```bea5cd5d```](https://github.com/ktmeaton/plague-phylogeography/commit/bea5cd5d) Database created
+* [```dd202409```](https://github.com/ktmeaton/plague-phylogeography/commit/dd202409) Code reformat
+* [```1e7ff9c0```](https://github.com/ktmeaton/plague-phylogeography/commit/1e7ff9c0) Data acquisition doc
+* [```82eed2aa```](https://github.com/ktmeaton/plague-phylogeography/commit/82eed2aa) Update README.md