Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Be more flexible on attribute values in GTFs #1150

Merged
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

Conversation

pinin4fjords
Copy link
Member

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).

@github-actions GitHub Actions
Copy link

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!

@github-actions GitHub Actions
Copy link

github-actions bot commented Jan 3, 2024 •
edited
Loading

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
Closed
@drpatelh drpatelh mentioned this pull request Jan 3, 2024
Closed
drpatelh
drpatelh approved these changes Jan 3, 2024
View reviewed changes
Copy link
Member

@drpatelh drpatelh left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🏅

@drpatelh drpatelh merged commit b4c6c69 into dev Jan 3, 2024
29 checks passed
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
Merged
10 tasks
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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@drpatelh drpatelh drpatelh approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE error on iGenomes TAIR10
2 participants
@pinin4fjords @drpatelh