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Fix multiqc skip#438

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JoseEspinosa merged 2 commits intodevfrom
fix_multiqc_skip
Dec 23, 2024
Merged

Fix multiqc skip#438
JoseEspinosa merged 2 commits intodevfrom
fix_multiqc_skip

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@LeonHafner LeonHafner commented Dec 9, 2024 •
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When the skip_multiqc parameter is used, the pipeline attempts to generate output from a non-existent channel, resulting in an error. This PR resolves the issue by introducing an empty channel, ch_multiqc_report, to ensure the output is handled without errors.

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/chipseq 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@LeonHafner LeonHafner changed the base branch from master to dev December 9, 2024 16:00
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github-actions Bot commented Dec 9, 2024

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @LeonHafner,

It looks like this pull-request is has been made against the nf-core/chipseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/chipseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions Bot commented Dec 9, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a90d020

+| ✅ 235 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-10 08:56:50

@LeonHafner LeonHafner marked this pull request as ready for review December 9, 2024 16:05
JoseEspinosa
JoseEspinosa approved these changes Dec 23, 2024
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Thanks a lot for your contribution!
LGTM 🚀

@JoseEspinosa JoseEspinosa merged commit 73a5304 into dev Dec 23, 2024
@LeonHafner LeonHafner deleted the fix_multiqc_skip branch December 26, 2024 16:29
@LeonHafner LeonHafner mentioned this pull request Mar 6, 2025
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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@LeonHafner @JoseEspinosa
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