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fix: CLIN-2947 make resume work again #36

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merged 1 commit into from
Oct 21, 2024

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LysianeBouchard
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@LysianeBouchard LysianeBouchard commented Oct 18, 2024

Fix variable input in process BCFTOOLS_NORM causing resume problems
See #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

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • Reference Data Documentation in docs/reference_data.md is updated.
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@LysianeBouchard LysianeBouchard force-pushed the fix/clin-2947-make-resume-work-again branch from 0403a7d to 9573078 Compare October 18, 2024 17:20
@LysianeBouchard LysianeBouchard marked this pull request as ready for review October 18, 2024 17:52
@LysianeBouchard LysianeBouchard merged commit c31c086 into main Oct 21, 2024
3 checks passed
@LysianeBouchard LysianeBouchard deleted the fix/clin-2947-make-resume-work-again branch October 21, 2024 14:35
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2 participants