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Use pseudoalignment subworkflow components from nf-core/modules #1210

Merged
merged 13 commits into from
Feb 15, 2024
Merged

Use pseudoalignment subworkflow components from nf-core/modules #1210

merged 13 commits into from
Feb 15, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Feb 7, 2024 •
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This PR updates the pseudoalignment subworkflow to account for de-localised modules and associated community standards.

There are a couple of changes in behaviour:

  • Serialised R SummarizedExperiment objects (.rds) have '.SummarizedExperiment` in their file names in line with conventions with other modules outputting R objects.
  • I passed the sample sheet file through into the subworkflow so that it could be baked into the SummarizedExperiment objects. I think that potentially makes those objects quite a lot more useful, but this could be reversed.

If this passes muster, we can delocalise the subworkflow too.

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).

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github-actions bot commented Feb 7, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fbbffc5

+| ✅ 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 2024-02-14 18:58:39

@maxulysse
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Don't forget to update CHANGELOG

@maxulysse
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I do love where this is going

@pinin4fjords pinin4fjords changed the title Use tx2gene from nf-core/modules Use pseudoalignment subworkflow components from nf-core/modules Feb 14, 2024
maxulysse
maxulysse approved these changes Feb 15, 2024
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LGTM, don't forget CHANGELOG

@pinin4fjords
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pinin4fjords commented Feb 15, 2024 •
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LGTM, don't forget CHANGELOG

2ced034 :-)

@maxulysse
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LGTM, don't forget CHANGELOG

2ced034 :-)

must have missed it on my phone, sorry

@pinin4fjords
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Thanks @maxulysse !

@pinin4fjords pinin4fjords merged commit ee79bd3 into dev Feb 15, 2024
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This was referenced Feb 16, 2024
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@maxulysse maxulysse deleted the tx2gene_from_nfcore branch May 29, 2024 14:48
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@maxulysse maxulysse maxulysse approved these changes

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