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Update sortmerna usage #1231

Merged
merged 6 commits into from
Mar 5, 2024
Merged

Update sortmerna usage #1231

merged 6 commits into from
Mar 5, 2024

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maxulysse
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Following @pinin4fjords work in Riboseq

To merge after #1221

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/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).

@maxulysse maxulysse marked this pull request as draft March 4, 2024 18:19
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github-actions bot commented Mar 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 04b3581

+| ✅ 169 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   7 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
  • 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
  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • 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 ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • 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 2.13.1
  • Run at 2024-03-05 09:20:13

@maxulysse maxulysse marked this pull request as ready for review March 4, 2024 19:11
pinin4fjords
pinin4fjords approved these changes Mar 5, 2024
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Looks good mostly- you just need to fix that import

workflows/rnaseq/main.nf Outdated Show resolved Hide resolved
subworkflows/local/prepare_genome/main.nf Outdated Show resolved Hide resolved
@maxulysse maxulysse merged commit 34e51dd into nf-core:dev Mar 5, 2024
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@maxulysse maxulysse deleted the sortmerna branch March 5, 2024 09:27
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

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@maxulysse @pinin4fjords