Closed LysianeBouchard closed 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
nf-core lint
nextflow run . -profile test,docker --outdir <OUTDIR>
nextflow run . -profile debug,test,docker --outdir <OUTDIR>
docs/usage.md
docs/output.md
docs/reference_data.md
CHANGELOG.md
README.md
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.
I did the equivalent in juno:
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.docs/reference_data.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).