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Fix bug using whitelist parameter #466

Merged
merged 4 commits into from Feb 5, 2024
Merged

Fix bug using whitelist parameter #466

merged 4 commits into from Feb 5, 2024

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rannick
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@rannick rannick commented Feb 2, 2024 •
edited

Fix an issue with channel i/o when using whitelist parameter, Closes #462

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
  • If necessary, also make a PR on the nf-core/rnafusion branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@rannick rannick changed the title add dump and rewrite channel Fix bug using whitelist parameter Feb 2, 2024
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github-actions bot commented Feb 2, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2988e8f

+| ✅ 171 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in WorkflowRnafusion.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-05 09:30:18

@rannick rannick requested a review from fevac February 5, 2024 08:49
@rannick rannick marked this pull request as draft February 5, 2024 08:50
fevac
fevac approved these changes Feb 5, 2024
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Lgtm! but don't forget to update the change log and please test with the small case before merging

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rannick commented Feb 5, 2024 •
edited

Test with whitelist parameters:

[f0/485039] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONCATCHER_WORKFLOW:FUSIONCATCHER (tendergoose)
[ed/1f36e3] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STAR_FOR_STARFUSION (tendergoose)
[8b/abe251] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:STAR_FOR_ARRIBA (tendergoose)
[73/e8a2c8] Submitted process > NFCORE_RNAFUSION:RNAFUSION:TRIM_WORKFLOW:FASTQC_FOR_FASTP (tendergoose)
[41/bcf926] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:SAMTOOLS_SORT_FOR_ARRIBA (tendergoose)
[90/578170] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA (tendergoose)
[92/b32fd7] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:SAMTOOLS_INDEX_FOR_STARFUSION (tendergoose)
[f4/39d0b5] Submitted process > NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PICARD_COLLECTINSERTSIZEMETRICS (tendergoose)
[98/7bc90b] Submitted process > NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:GATK4_MARKDUPLICATES (tendergoose)
[99/0d5b8a] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (tendergoose)
[3b/71ee70] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:SAMTOOLS_VIEW_FOR_ARRIBA (tendergoose)
[fe/308948] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:SAMTOOLS_VIEW_FOR_STARFUSION (tendergoose)
[54/8bf0dd] Submitted process > NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PICARD_COLLECTRNASEQMETRICS (tendergoose)
[9f/4f337e] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:SAMTOOLS_INDEX_FOR_ARRIBA (tendergoose)
[64/a17cc0] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:SAMTOOLS_INDEX_FOR_STARFUSION_CRAM (tendergoose)
[23/1fe241] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONREPORT_WORKFLOW:FUSIONREPORT (tendergoose)
Pulling Singularity image https://depot.galaxyproject.org/singularity/pigz:2.3.4 
[4b/314f79] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:CAT_CAT (tendergoose)
[98/f875f9] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tendergoose)
[37/11c5b9] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (tendergoose)
[6f/af7eba] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tendergoose)
[c5/f312e8] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:VCF_COLLECT (tendergoose)
[d4/cbebc6] Submitted process > NFCORE_RNAFUSION:RNAFUSION:CUSTOM_DUMPSOFTWAREVERSIONS (1)
[49/2473b9] Submitted process > NFCORE_RNAFUSION:RNAFUSION:MULTIQC
-[nf-core/rnafusion] Pipeline completed successfully-
-[nf-core/rnafusion] Pipeline completed successfully-

@rannick rannick marked this pull request as ready for review February 5, 2024 09:28
@rannick rannick merged commit abcc7a8 into dev Feb 5, 2024
6 checks passed
@rannick rannick deleted the fix_whitelist branch February 5, 2024 09:52
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