storeDir option doesn't work for all modules

[anoronh4]

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: https://github.com/mskcc/tempo/blob/cd3ce1364481e474f70639b8b9da51412b99a6e6/pipeline.nf#L583-L585 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]

Other processes in dsl2 Tempo (outside of alignment_wf) that need to be adjusted include:

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

(this list may be updated)