From 596d55c381de5ac3c9ad00639e6712091449f8b7 Mon Sep 17 00:00:00 2001 From: Katherine Eaton Date: Tue, 2 Mar 2021 18:52:55 -0500 Subject: [PATCH] finish notes for v0.2.5 --- CHANGELOG.md | 46 +++++++++++++++++++++++++++++++++ docs/notes/Notes_Development.md | 17 ------------ docs/notes/Notes_v0.2.5.md | 16 ++++++++++++ 3 files changed, 62 insertions(+), 17 deletions(-) create mode 100644 docs/notes/Notes_v0.2.5.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 52fac12cd..2a5a49dec 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,51 @@ ### Commits +## v0.2.5 + +### Notes + +1. Separate mugration notebook into model and plot. +1. Add a heatmap test, output to misc. +1. Create a new rule to generate locus coverage. +1. Remove output directory of eager rule. +1. Make a list of target genes +1. Hard code target genes into ref locus bed +1. Move ref locus bed to reference +1. Create gene by gene coverage. +1. Analyze both coverage and depth of loci. +1. Compare gene to plasmid coverage (pla, pPCP1) +1. Apply a coverage filter for pPCP1 plasmid. +1. Add locus coverage info to nexus tree. +1. Created spreadmaps for branch major. + +### 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 + ## v0.2.4 ### Notes @@ -16,6 +61,7 @@ ### 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 diff --git a/docs/notes/Notes_Development.md b/docs/notes/Notes_Development.md index 016023c85..f32361c43 100644 --- a/docs/notes/Notes_Development.md +++ b/docs/notes/Notes_Development.md @@ -1,22 +1,5 @@ # Development -1. Separate mugration notebook into model and plot. -1. Add a heatmap test, output to misc. -1. Create a new rule to generate locus coverage. -1. Remove output directory of eager rule. -1. Make a list of target genes - - pPCP1 - pla (AL109969,6665,7603,pla) -1. Hard code target genes into ref locus bed -1. Move ref locus bed to reference -1. Create gene by gene coverage. -1. Analyze both coverage and depth of loci. -1. Compare gene to plasmid coverage (pla, pPCP1) -1. Apply a coverage filter for pPCP1 plasmid. -1. Add locus coverage info to nexus tree. -1. Created spreadmaps for branch major. - -## TO-DO - 1. Add locus coverage output to report. 1. Check if multiqc still runs without eager output dir... 1. Add latvia samples to database! diff --git a/docs/notes/Notes_v0.2.5.md b/docs/notes/Notes_v0.2.5.md new file mode 100644 index 000000000..63861dd43 --- /dev/null +++ b/docs/notes/Notes_v0.2.5.md @@ -0,0 +1,16 @@ +# v0.2.5 + +1. Separate mugration notebook into model and plot. +1. Add a heatmap test, output to misc. +1. Create a new rule to generate locus coverage. +1. Remove output directory of eager rule. +1. Make a list of target genes + - pPCP1 - pla (AL109969,6665,7603,pla) +1. Hard code target genes into ref locus bed +1. Move ref locus bed to reference +1. Create gene by gene coverage. +1. Analyze both coverage and depth of loci. +1. Compare gene to plasmid coverage (pla, pPCP1) +1. Apply a coverage filter for pPCP1 plasmid. +1. Add locus coverage info to nexus tree. +1. Created spreadmaps for branch major.