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storeDir option doesn't work for all modules #1000

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anoronh4 opened this issue Dec 22, 2023 · 1 comment · May be fixed by #1001
Open

storeDir option doesn't work for all modules #1000

anoronh4 opened this issue Dec 22, 2023 · 1 comment · May be fixed by #1001
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When testing the storeDir option with tempo, not all processes successfully cache. For example i get the message:

WARN: [RunBQSR (s_C_5DD7V7_N001_d)] StoreDir can only be used when using 'file' outputs

This means that every time we want to restart tempo for some reason, RunBQSR will be re-run for every sample, even when using the -resume option. I think the reason this happens is because of these lines of code:

tempo/pipeline.nf

Lines 583 to 585 in cd3ce13

output:
set idSample, target, file("${idSample}.bam"), file("${idSample}.bam.bai") into bamsBQSR4Alfred, bamsBQSR4CollectHsMetrics, bamsBQSR4Tumor, bamsBQSR4Normal, bamsBQSR4QcPileup, bamsBQSR4Qualimap
set idSample, target, val("${file(outDir).toString()}/bams/${idSample}/${idSample}.bam"), val("${file(outDir).toString()}/bams/${idSample}/${idSample}.bam.bai") into bamResults

The variables idSample and target are already in the process context, but the others are not. This might be easily adjustable. I have not tested this yet with non-alignment processes, so i don't have a complete view of which processes cannot be cached when using storeDir
@anoronh4 anoronh4 linked a pull request Dec 28, 2023 that will close this issue
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@anoronh4 anoronh4 self-assigned this Jan 26, 2024
@anoronh4 anoronh4 mentioned this issue Jan 30, 2024
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anoronh4 commented Jan 30, 2024 •
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Other processes in dsl2 Tempo (outside of alignment_wf) that need to be adjusted include:

  • facets_wf:DoFacets
  • loh_wf:RunPolysolver
  • loh_wf:RunLOHHLA
  • snv_wf:RunNeoantigen
  • validate_wf:CrossValidateSamples (just exclude this from storeDir since there are no file outputs and it does not need caching)
  • samplePairingQC_wf:QcConpair
  • sampleQC_wf:QcConpairAll
  • hrdetect_wf:HRDetect
  • mdParse_wf:MetaDataParser
  • snv_wf:SomaticFacetsAnnotation
  • sv_wf:SomaticAnnotateSVBedpe
  • sv_wf:SomaticRunClusterSV
  • clonality_wf:SomaticRunSVclone
  • germlineSNV_wf:GermlineRunStrelka2
  • germlineSNV_wf:GermlineFacetsAnnotation
  • germlineSNV_wf:GermlineCombineHaplotypecallerVcf

(this list may be updated)

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allow storeDir for RunBQSR mskcc/tempo
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