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Be more flexible on attribute values in GTFs #1150

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merged 5 commits into from
Jan 3, 2024
Merged

Be more flexible on attribute values in GTFs #1150

merged 5 commits into from
Jan 3, 2024

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pinin4fjords
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Closes #1132

In the above noted issue, parsing a GTF file failed due to semicolons in the attribute value. We can address this by being more flexible on field content while being stricter on the formatting of the attribute line itself.

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>).
  • 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 Jan 3, 2024

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!

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github-actions bot commented Jan 3, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 87f603c

+| ✅ 146 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • 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: lib/NfcoreTemplate.groovy
  • 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 - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-03 18:41:02

@pinin4fjords pinin4fjords linked an issue Jan 3, 2024 that may be closed by this pull request
NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE error on iGenomes TAIR10 #1132
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@drpatelh drpatelh mentioned this pull request Jan 3, 2024
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drpatelh
drpatelh approved these changes Jan 3, 2024
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🏅

@drpatelh drpatelh merged commit b4c6c69 into dev Jan 3, 2024
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pinin4fjords added a commit that referenced this pull request Jan 4, 2024
@pinin4fjords
fix to #1150
05cc397
@pinin4fjords pinin4fjords mentioned this pull request Jan 4, 2024
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drpatelh added a commit that referenced this pull request Jan 4, 2024
@drpatelh
Merge pull request #1151 from nf-core/fix_gtf_flexibility
cd3a4f5 
fix to #1150: reinstate conditional
@pinin4fjords pinin4fjords deleted the flexible_tx2gene branch January 4, 2024 10:23
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@drpatelh drpatelh drpatelh approved these changes

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NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE error on iGenomes TAIR10
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