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Publish coverage files #331

Merged
merged 2 commits into from
Aug 22, 2023
Merged

Publish coverage files #331

merged 2 commits into from
Aug 22, 2023

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FelixKrueger
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For NOMe-seq runs, the coverage2cytosine module produces both CpG_report.txt.gz and GpC_report.txt.gz text files; in addition, it also generates these information in the form of coverage files (ending in *.cov.gz), however these files do not get published at all.

This PR adds a new publishing rule for CpG/GpC coverage files.

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/methylseq 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).

@FelixKrueger
Update modules.config
9e2d80f 
Adding publish mode for coverage2cytosine NOMe-seq filtered GpC coverage files.
@FelixKrueger
Update CHANGELOG.md
107f736 
Added comment for coverage2cytosine publishing of files.
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github-actions bot commented Jul 31, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 107f736

+| ✅ 147 tests passed       |+
#| ❔   3 tests were ignored |#
-| ❌   8 tests failed       |-

❌ Test failures:

  • nextflow_config - Config variable not found: params.validationShowHiddenParams
  • nextflow_config - Config variable not found: params.validationSchemaIgnoreParams
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
  • files_unchanged - assets/nf-core-methylseq_logo_light.png does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • schema_params - Param schema_ignore_params from nextflow config not found in nextflow_schema.json
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-25 14:02:03

ewels
ewels approved these changes Aug 22, 2023
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LGTM, thanks!

CI failures are because we need to update the template. See other PRs.

@ewels ewels merged commit e576ec8 into nf-core:dev Aug 22, 2023
9 of 10 checks passed
@edmundmiller edmundmiller added this to the 2.5.0 milestone Aug 25, 2023
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@ewels ewels ewels approved these changes

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@FelixKrueger @ewels @edmundmiller