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Updating nf-core-modules #685

Merged
merged 8 commits into from
Jul 28, 2022
Merged

Updating nf-core-modules #685

merged 8 commits into from
Jul 28, 2022

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asp8200
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@asp8200 asp8200 commented Jul 25, 2022

#684

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 25, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9118d64

+| ✅ 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 2022-07-28 08:56:08

@asp8200 asp8200 requested a review from SusiJo July 25, 2022 13:41
@asp8200 asp8200 mentioned this pull request Jul 25, 2022
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SusiJo commented Jul 26, 2022

Hey @asp8200,
There was already a PR to update the modules which was not merged in the end. There were some questions and concerns of @maxulysse and @FriederikeHanssen. Are these clarified now?

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asp8200 commented Jul 27, 2022 •
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Hey @asp8200, There was already a PR to update the modules which was not merged in the end. There were some questions and concerns of @maxulysse and @FriederikeHanssen. Are these clarified now?

@SusiJo : I wasn't aware of your PR. @maxulysse asked me to update the modules so I went ahead with that.

I had a discussion with @maxulysse about whether it was okay to just pass the empty list [], instead of a target-bed, as the second paramenter to BCFTOOLS_STATS in subworkflows/nf-core/vcf_qc.nf (#686 (comment)). We agreed that it was okay for now, and that it could be fixed in a later PR - if necessary.

Now I don't know whether this PR should be merged or we should try to revive @SusiJo 's PR. Let me know your opinion :-)

@asp8200 asp8200 marked this pull request as ready for review July 27, 2022 17:59
@asp8200 asp8200 requested a review from maxulysse as a code owner July 27, 2022 17:59
@asp8200 asp8200 requested a review from SusiJo July 27, 2022 19:14
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SusiJo commented Jul 28, 2022

No please go ahead :) My PR did not update the other modules, like yours.

SusiJo
SusiJo reviewed Jul 28, 2022
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maxulysse approved these changes Jul 28, 2022
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LGTM.
Let's try out this stageAs: "?/*"

@asp8200 asp8200 merged commit 89d1574 into nf-core:dev Jul 28, 2022
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@asp8200 @SusiJo @maxulysse