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wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL
MIT License
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Metrics files #107

Closed chrisamiller closed 1 year ago

chrisamiller commented 1 year ago

Right now, there are two metrics files that aren't getting spit out in the final results from the immuno pipeline.

1) we're not generating a flagstat for the RNAseq bam (or if we are, we're not outputting it) 2) we're not keeping the markduplicates metrics file.

Both should be easy enough to add and dump out.

chrisamiller commented 1 year ago

You know what, I take it back. The old picard method for marking duplicates used to spit out more detailed information. This one just gives the number of dups, which is the same information that can be seen in the flagstat for the bam, so no reason that it should need to be output.

I do still think a generating a flagstat for the rna bam would be a good idea