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Add Leafcutter tool #161

Merged
merged 13 commits into from
Nov 26, 2024
Merged

Add Leafcutter tool #161

merged 13 commits into from
Nov 26, 2024

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lpantano
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@lpantano lpantano commented Nov 21, 2024 •
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Add first steps of leaf cutter splicing quantification to the pipeline.

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/rnasplice 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).

@github-actions GitHub Actions
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Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@lpantano lpantano marked this pull request as ready for review November 22, 2024 20:48
mashehu
mashehu requested changes Nov 25, 2024
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@github-actions GitHub Actions
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github-actions bot commented Nov 26, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit b8e3a4f

+| ✅ 250 tests passed       |+
!| ❗   3 tests had warnings |!
-| ❌  12 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/WorkflowRnasplice.groovy
  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - docs/images/nf-core-rnasplice_logo_dark.png does not match the template
  • multiqc_config - assets/multiqc_config.yml does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="/~https://github.com/nf-core/rnasplice/tree/dev" target="_blank">nf-core/rnasplice</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnasplice/dev/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="/~https://github.com/nf-core/rnasplice/releases/tag/1.0.4" target="_blank">nf-core/rnasplice</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnasplice/1.0.4/docs/output" target="_blank">documentation</a>.
  • modules_config - conf/modules.config contains withName:CAT_ADDITIONAL_FASTA, but the corresponding process is not present in any of the Nextflow scripts.

❗ Test warnings:

  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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 WorkflowRnasplice.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-11-26 17:10:25

@mashehu
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mashehu commented Nov 26, 2024

fixed the linting action. just guessed what the current template version for this pipeline code is. please change the version in .nf-core.yml to the actual version, so the linting is a bit more precise.

lpantano and others added 2 commits November 26, 2024 11:26
@lpantano @mashehu
add regular expression to list of genes
77e25d2 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@lpantano
add missing coma
466013d
@nvnieuwk
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I'll merge this, the linting will be fixed in another PR

@nvnieuwk nvnieuwk merged commit afd559f into dev Nov 26, 2024
19 of 20 checks passed
@nvnieuwk nvnieuwk deleted the leafcutter branch November 26, 2024 19:22
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@mashehu mashehu mashehu approved these changes

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4 participants
@lpantano @mashehu @nvnieuwk @abartlett004