Recent Releases of popglen
popglen - 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: https://github.com/zjnolen/PopGLen/compare/v0.4.0...v0.4.1
- Python
Published by zjnolen over 1 year ago
popglen - 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 https://github.com/zjnolen/PopGLen/pull/47
- Fix: Make it so that bamlist generation is re-run if sample order changes, keeping meta-data consistent by @zjnolen in https://github.com/zjnolen/PopGLen/pull/51
- Add in frequency based functionalities of NgsRelate (and add allele frequencies as a targeted output as a byproduct) by @zjnolen in https://github.com/zjnolen/PopGLen/pull/52
- Prepare v0.4.0 by @zjnolen in https://github.com/zjnolen/PopGLen/pull/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: https://github.com/zjnolen/PopGLen/compare/v0.3.0...v0.4.0
- Python
Published by zjnolen over 1 year ago
popglen - 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.
What's Changed
- Change overlap clipping method (fgbio -> bamutil) by @zjnolen in https://github.com/zjnolen/PopGLen/pull/17
- Update depth filters by @zjnolen in https://github.com/zjnolen/PopGLen/pull/18
- Pileup mappability by @zjnolen in https://github.com/zjnolen/PopGLen/pull/19
- Set up so workflow can start with bam files and only perform popgen analyses by @zjnolen in https://github.com/zjnolen/PopGLen/pull/21
- Switch default aligner for historical samples from bwa mem to aln by @zjnolen in https://github.com/zjnolen/PopGLen/pull/20
- Allow user input repeat bed files by @zjnolen in https://github.com/zjnolen/PopGLen/pull/23
- Enable download of FASTQ files from NCBI/ENA when an SRA accession is supplied by @zjnolen in https://github.com/zjnolen/PopGLen/pull/24
- Make it so reads are only collapsed for historical samples by @zjnolen in https://github.com/zjnolen/PopGLen/pull/25
- Enable subsampling to lower depth by @zjnolen in https://github.com/zjnolen/PopGLen/pull/26
- Move from prunengsLD.py to prunegraph for pruning by @zjnolen in https://github.com/zjnolen/PopGLen/pull/30
- Allow polarizing SFS to ancestral states by @zjnolen in https://github.com/zjnolen/PopGLen/pull/31
- Enable changing -doMajorMinor and -doMaf in Beagle (and maf file) calculation by @zjnolen in https://github.com/zjnolen/PopGLen/pull/32
- ngsF-HMM implementation improvements by @zjnolen in https://github.com/zjnolen/PopGLen/pull/34
- Allow generating bootstrapped SFS. Includes estimating confidence intervals for heterozygosity by @zjnolen in https://github.com/zjnolen/PopGLen/pull/35
- Samtools subsample is done only on reads passing mapQ by @zjnolen in https://github.com/zjnolen/PopGLen/pull/36
- Fix: Ensure libraries are deduped separately in historical samples by @zjnolen in https://github.com/zjnolen/PopGLen/pull/37
- Allow filtering with -minInd in ANGSD by @zjnolen in https://github.com/zjnolen/PopGLen/pull/38
- Add in ability to remove transitions easily from config by @zjnolen in https://github.com/zjnolen/PopGLen/pull/39
- Allow removal of individuals from dataset when subsampling by @zjnolen in https://github.com/zjnolen/PopGLen/pull/40
- Add ref bias calculation by @zjnolen in https://github.com/zjnolen/PopGLen/pull/44
- Allow multiple target depths for depth subsampling by @zjnolen in https://github.com/zjnolen/PopGLen/pull/46
Full Changelog: https://github.com/zjnolen/PopGLen/compare/v0.2.0...v0.3.0
- Python
Published by zjnolen over 1 year ago
popglen - v0.2.0
What's Changed
- Convert depth filter to be median based by @zjnolen in https://github.com/zjnolen/angsd-snakemake-pipeline/pull/11
- Calculating GLs on SAF and beagle generation by @zjnolen in https://github.com/zjnolen/angsd-snakemake-pipeline/pull/12
- Add IBSrelate IBS method by @zjnolen in https://github.com/zjnolen/angsd-snakemake-pipeline/pull/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: https://github.com/zjnolen/angsd-snakemake-pipeline/compare/v0.1.0...v0.2.0
- Python
Published by zjnolen over 2 years ago
popglen - v0.1.0
What's Changed
- Attempt to fix Github actions failing due to space by @zjnolen in https://github.com/zjnolen/angsd-snakemake-pipeline/pull/3
- Performing SNP calling and linkage pruning per pop before ngsF-HMM by @zjnolen in https://github.com/zjnolen/angsd-snakemake-pipeline/pull/7
- Convert rules to wrappers where possible by @zjnolen in https://github.com/zjnolen/angsd-snakemake-pipeline/pull/6
- Migrate to using prune_graph for LD pruning by @zjnolen in https://github.com/zjnolen/angsd-snakemake-pipeline/pull/8
- Allow processing of multiple sequencing runs per sample by @zjnolen in https://github.com/zjnolen/angsd-snakemake-pipeline/pull/9
- Merge in full changes for v0.1 by @zjnolen in https://github.com/zjnolen/angsd-snakemake-pipeline/pull/10
Full Changelog: https://github.com/zjnolen/angsd-snakemake-pipeline/compare/v0.1.0-alpha...v0.1.0
- Python
Published by zjnolen over 2 years ago
popglen - v0.1.0-alpha
Release an alpha version for testing deployment and to build first stable release off of.
- Python
Published by zjnolen over 2 years ago