Add FDA metrics subworkflow to Immuno pipeline

wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL

MIT License

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Add FDA metrics subworkflow to Immuno pipeline #78

Closed tmooney closed 1 year ago

tmooney commented 1 year ago

This incorporates some recent additions to the genome/analysis-workflows immuno.cwl pipeline into the WDL version here.

malachig commented 1 year ago

hi @tmooney . My one request for this PR is that we not leave all these FDA results at the top level of the results dir:

aligned_normal_dna_fda_metrics
aligned_tumor_dna_fda_metrics
aligned_tumor_rna_fda_metrics
unaligned_normal_dna_fda_metrics
unaligned_tumor_dna_fda_metrics
unaligned_tumor_rna_fda_metrics

Instead can we place all of this under the existing qc or in a dedicated subdir at the toplevel.

i.e. one of these options

qc/fda_metrics/
fda_metrics/

tmooney commented 1 year ago

Updated the outputs to build a struct named fda_metrics to group these metrics together. (Pushed the commit yesterday; a test run completed overnight.)

malachig commented 1 year ago

My tests with the updated version of this PR have succeeded. When I pull down the results, the FDA QC results appear nicely organized. Looks good to me!