Ferlab-Ste-Justine / Post-processing-Pipeline

Variant analysis for genome and exome VGCFs
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fix: CLIN-2947 make resume work again #36

Closed LysianeBouchard closed 1 month ago

LysianeBouchard commented 1 month ago

Fix variable input in process BCFTOOLS_NORM causing resume problems See https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/issues/31

Test

I run the following commands locally. In the second command (with resume), as expected, all process were marked as "cached", except for the writemeta.

nextflow run main.nf -profile docker,test
nextflow run main.nf -profile docker,test -resume

I did the equivalent in juno:

kubectl exec -it -n cqdg-prod deploy/nextflow -- /bin/bash

 cd  pipeline/dev/Post-processing-Pipeline/

nextflow -c /root/nextflow/config/fusion.config run Ferlab-Ste-Justine/Post-processing-Pipeline -r fix/clin-2947-make-resume-work-again -params-file data-test/paramsJuno.json -work-dir 's3://cqdg-prod-file-scratch/nextflow/scratch/lysiane'  

nextflow -c /root/nextflow/config/fusion.config run Ferlab-Ste-Justine/Post-processing-Pipeline -r fix/clin-2947-make-resume-work-again -params-file data-test/paramsJuno.json -work-dir 's3://cqdg-prod-file-scratch/nextflow/scratch/lysiane'  -resume

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