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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

MIT License

63 stars 30 forks source link

Dev #32

Closed cademirch closed 2 years ago

cademirch commented 2 years ago

Fair amount of additions here.

Added @erikenbody's QC rules
Added config option for splitting by Ns. If false, then each contig will be its own interval for parallelization. Closes #23.
Added logic to handle local fastq files. Can be specified by adding fq1 and fq2 column to samples sheet. Closes #21.
Changed github actions to test local files as well as QC rules
- Separate action workflow for QC rules since it needs a bigger dataset, only runs if qc.smk is changed.

tsackton commented 2 years ago

@cademirch @erikenbody lots of great stuff in here! Let's get this merged into main ASAP. I have seen a few issues that will need to be fixed / addressed but easiest, I think, to start a pull request from dev -> main and then work through the pull request review to solve any outstanding issues.

If one of you can start that pull request ASAP I'll start adding my comments.