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Fix resume #66

Merged
merged 3 commits into from
Aug 4, 2023
Merged

Fix resume #66

merged 3 commits into from
Aug 4, 2023

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mirpedrol
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Summary modules were modifying the input file. This made the resume break on these modules.
They now generate a new file instead of modifying the input, fixing the catching of these modules.

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/crisprseq 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 Aug 3, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 05f4f72

+| ✅ 156 tests passed       |+
#| ❔  16 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-04 11:14:07

mirpedrol
mirpedrol commented Aug 3, 2023
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CHANGELOG.md Outdated Show resolved Hide resolved
@mirpedrol mirpedrol mentioned this pull request Aug 4, 2023
Merged
10 tasks
@mirpedrol mirpedrol merged commit c6b9910 into nf-core:dev Aug 4, 2023
9 of 10 checks passed
@mirpedrol mirpedrol deleted the fix-resume-modules branch August 4, 2023 11:54
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@LaurenceKuhl LaurenceKuhl LaurenceKuhl approved these changes

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@mirpedrol @LaurenceKuhl