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Fix intermediate files published #681

Merged
merged 4 commits into from
Jul 22, 2022
Merged

Fix intermediate files published #681

merged 4 commits into from
Jul 22, 2022

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maxulysse
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Will close #680

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/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 --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).

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github-actions bot commented Jul 22, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 910440f

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-22 09:22:28

@maxulysse
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Good news, as I extended the checks, I could see that only Freebayes was producting unexpected files

@maxulysse maxulysse merged commit e09f18a into nf-core:dev Jul 22, 2022
@maxulysse maxulysse deleted the dev_freebayes branch July 22, 2022 13:14
FriederikeHanssen
FriederikeHanssen reviewed Jul 22, 2022
View reviewed changes
conf/modules.config
@@ -607,6 +607,9 @@ process{
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.simpleName}" }
ext.args = '--min-alternate-fraction 0.1 --min-mapping-quality 1'
ext.when = { params.tools && params.tools.split(',').contains('freebayes') }
publishDir = [
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why is this happening though? shouldn't publishing be disabled by default?

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I agree but it was

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I believe you :D just wondering if something else is going on somewhere.

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I'm sure something else is going on. I'll check it more more in detail next week

@asp8200 asp8200 mentioned this pull request Jul 25, 2022
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@mahesh-panchal mahesh-panchal mahesh-panchal approved these changes

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@maxulysse @FriederikeHanssen @mahesh-panchal