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:

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]

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)