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aryarm / as_analysis

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq
MIT License
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skipping the variant calling pipeline within the master pipeline #53

Closed aryarm closed 4 years ago

aryarm commented 4 years ago

It should be possible to have the master Snakefile skip the variant calling pipeline based on the inputs that have been provided it. This will require a major refactor, but the result will be that users probably won't ever have to worry about executing any of the subworkflows on their own. They'll just have to switch out the config files!

We could also use this as an opportunity to tackle issues #18, #22, #48, #51, and #52

aryarm commented 4 years ago

this is done. users can skip the variant calling pipeline by executing the WASP pipeline on its own, which now also executes the counts pipeline automatically