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Delocalise catadditionalfasta #1216

Merged
merged 12 commits into from
Feb 16, 2024
Merged

Delocalise catadditionalfasta #1216

merged 12 commits into from
Feb 16, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Feb 16, 2024 •
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Move the cat_additional_fasta to the one in nf-core.

PR checklist

Closes #1162

  • 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/rnaseq 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).

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github-actions bot commented Feb 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4ad0bba

+| ✅ 169 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowRnaseq.groovy
  • 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:

  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File does not exist: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-16 13:57:51

@pinin4fjords pinin4fjords linked an issue Feb 16, 2024 that may be closed by this pull request
Migrate CAT_ADDITIONAL_FASTA module to nf-core/modules #1162
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@pinin4fjords pinin4fjords merged commit f4436b3 into dev Feb 16, 2024
27 checks passed
@pinin4fjords pinin4fjords deleted the delocalise_catadditionalfasta branch February 16, 2024 15:19
@pinin4fjords pinin4fjords mentioned this pull request Feb 16, 2024
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@maxulysse maxulysse maxulysse approved these changes

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Migrate CAT_ADDITIONAL_FASTA module to nf-core/modules
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@pinin4fjords @maxulysse