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Fix param arg_amrfinderplus_name #371

Merged
merged 2 commits into from
May 3, 2024
Merged

Fix param arg_amrfinderplus_name #371

merged 2 commits into from
May 3, 2024

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m3hdad
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@m3hdad m3hdad commented May 3, 2024

Module configuration could not read meta.id if --arg_amrfinderplus_name is set true.
ext.args at module.conf needs to be wrapped in curly brackets and double quotation around --name ${meta.id}.

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/funcscan 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.
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jasmezz
jasmezz approved these changes May 3, 2024
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LGTM now, wait for CI checks to succeed.

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github-actions bot commented May 3, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 59e67c9

+| ✅ 236 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-03 08:25:37

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jasmezz commented May 3, 2024

Note: The linting check is failing due to a subworkflow update on the nf-core side. I fixed that already on the dev branch. Since it's only that linting check and no relevant functionality that would impact your PR, I'll merge this here now anyway.

@jasmezz jasmezz merged commit f63f569 into nf-core:dev May 3, 2024
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@jasmezz jasmezz mentioned this pull request Jul 29, 2024
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