v0.4.1

Update 24-11-12: The bug that was introduced in Snakemake 8.25.1 that caused bash scripts to fail has been fixed in 8.25.3, so versions of Snakemake >= 8.25.3 should work now.

Bug fix: explicitly set Snakemake version to 8.25.0 in the environment, which has been tested to be fully working with this workflow.

Full Changelog: v0.4.0...v0.4.1

v0.4.0

With v0.4.0, PopGLen is largely ready for use and all planned components have been added in. If you would like to suggest a feature or report a bug, please submit an issue.

What's Changed

• Containerize all rules and use as minimal containers as possible by @zjnolen in #47
• Fix: Make it so that bamlist generation is re-run if sample order changes, keeping meta-data consistent by @zjnolen in #51
• Add in frequency based functionalities of NgsRelate (and add allele frequencies as a targeted output as a byproduct) by @zjnolen in #52
• Prepare v0.4.0 by @zjnolen in #50 which includes many updates to improve reporting figures, clean ups of resource usage, and most importantly a large update to documentation, including finishing the tutorial dataset.

Full Changelog: v0.3.0...v0.4.0

v0.3.0

With v0.3.0, the pipeline is largely working, and should be usable for many datasets performing the analyses described in the readme. Work will continue on the develop branch, focused on optimizing how certain analyses are done, improving resource allocation, and improving documentation.

Documentation for v0.3.0

What's Changed

• Change overlap clipping method (fgbio -> bamutil) by @zjnolen in #17
• Update depth filters by @zjnolen in #18
• Pileup mappability by @zjnolen in #19
• Set up so workflow can start with bam files and only perform popgen analyses by @zjnolen in #21
• Switch default aligner for historical samples from bwa mem to aln by @zjnolen in #20
• Allow user input repeat bed files by @zjnolen in #23
• Enable download of FASTQ files from NCBI/ENA when an SRA accession is supplied by @zjnolen in #24
• Make it so reads are only collapsed for historical samples by @zjnolen in #25
• Enable subsampling to lower depth by @zjnolen in #26
• Move from prune_ngsLD.py to prune_graph for pruning by @zjnolen in #30
• Allow polarizing SFS to ancestral states by @zjnolen in #31
• Enable changing -doMajorMinor and -doMaf in Beagle (and maf file) calculation by @zjnolen in #32
• ngsF-HMM implementation improvements by @zjnolen in #34
• Allow generating bootstrapped SFS. Includes estimating confidence intervals for heterozygosity by @zjnolen in #35
• Samtools subsample is done only on reads passing mapQ by @zjnolen in #36
• Fix: Ensure libraries are deduped separately in historical samples by @zjnolen in #37
• Allow filtering with -minInd in ANGSD by @zjnolen in #38
• Add in ability to remove transitions easily from config by @zjnolen in #39
• Allow removal of individuals from dataset when subsampling by @zjnolen in #40
• Add ref bias calculation by @zjnolen in #44
• Allow multiple target depths for depth subsampling by @zjnolen in #46

Full Changelog: v0.2.0...v0.3.0

v0.2.0

What's Changed

• Convert depth filter to be median based by @zjnolen in #11
• Calculating GLs on SAF and beagle generation by @zjnolen in #12
• Add IBSrelate IBS method by @zjnolen in #15

Bug fixes

• Fix issue where last chromosome would be excluded
• Inbreeding coefficient calculation no longer includes table header (leaving last entry out)
• Plotting Tajima's will generate blank plot for 1 sample populations rather than failing

Full Changelog: v0.1.0...v0.2.0

v0.1.0

What's Changed

• Attempt to fix Github actions failing due to space by @zjnolen in #3
• Performing SNP calling and linkage pruning per pop before ngsF-HMM by @zjnolen in #7
• Convert rules to wrappers where possible by @zjnolen in #6
• Migrate to using prune_graph for LD pruning by @zjnolen in #8
• Allow processing of multiple sequencing runs per sample by @zjnolen in #9
• Merge in full changes for v0.1 by @zjnolen in #10

Full Changelog: v0.1.0-alpha...v0.1.0

v0.1.0-alpha

Release an alpha version for testing deployment and to build first stable release off of.