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update all modules for correct registry usage #1032

Merged
merged 19 commits into from
May 24, 2023
Merged

update all modules for correct registry usage #1032

merged 19 commits into from
May 24, 2023

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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 - 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).

@maxulysse
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  • check out local modules

@maxulysse
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@adamrtalbot how can you approve with so many stuff left to do here

@adamrtalbot adamrtalbot self-requested a review May 23, 2023 10:35
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@adamrtalbot how can you approve with so many stuff left to do here

Ah sorry I just reviewed the code that was there.

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github-actions bot commented May 23, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit bdae311

+| ✅ 153 tests passed       |+
#| ❔   9 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-24 15:34:17

FriederikeHanssen
FriederikeHanssen reviewed May 24, 2023
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conf/modules/trimming.config
@@ -17,7 +17,7 @@ process {

withName: 'FASTP' {
ext.args = [ "",
params.trim_fastq ?: "--disable_adapter_trimming",
!params.trim_fastq ? "--disable_adapter_trimming" : "", // Disable adapter trimming
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this shortly broke my brain :D

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I did it this way to have all "" properly aligned.
because of the elvis operator ?: we were actually displaying true in the args...

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I'm merging with the fallen tests for concatenate_vcfs singularity, and will investigate that in a separate PR

@maxulysse maxulysse merged commit 3bc3a1d into nf-core:dev May 24, 2023
@maxulysse maxulysse deleted the update_modules_registry branch May 24, 2023 20:31
This was referenced May 24, 2023
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@adamrtalbot adamrtalbot Awaiting requested review from adamrtalbot

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@maxulysse @adamrtalbot @FriederikeHanssen