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fix saveAs parameter for publishDir directive #529

Merged
merged 2 commits into from
Apr 29, 2022
Merged

fix saveAs parameter for publishDir directive #529

merged 2 commits into from
Apr 29, 2022

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maxulysse
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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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • 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).

JoseEspinosa
JoseEspinosa approved these changes Apr 29, 2022
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LGTM! 🚀

FriederikeHanssen
FriederikeHanssen reviewed Apr 29, 2022
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conf/modules.config
@@ -630,7 +637,7 @@ process{
enabled: !params.no_intervals,
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
pattern: "*{mpileup}"
pattern: "*mpileup"
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whys is the saveAs thing not here?

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because pattern

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Since you don't need it when you have a pattern, then the yml does not match it and thus is not published

@maxulysse maxulysse merged commit 787741d into nf-core:dev Apr 29, 2022
@maxulysse maxulysse deleted the dev_dont_publish_versions_yml branch April 29, 2022 15:37
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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3 participants
@maxulysse @JoseEspinosa @FriederikeHanssen