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

Fix pipeline failure when transcript_fasta not provided and skip_gtf_filter is set to TRUE #1126

Merged
merged 5 commits into from
Nov 20, 2023
Merged

Fix pipeline failure when transcript_fasta not provided and skip_gtf_filter is set to TRUE #1126

merged 5 commits into from
Nov 20, 2023

Conversation

RHReynolds
Copy link
Contributor

@RHReynolds RHReynolds commented Nov 20, 2023 •
edited
Loading

Fixes #1125

If the pipeline is run with the test profile, with no transcript fasta provided and --skip_gtf_filter enabled, it fails due to the following error:

Access to 'GTF_FILTER.out' is undefined since the process 'GTF_FILTER' has not been invoked before accessing the output attribute

 -- Check script '/Users/rreynolds/pipeline_development/nf-core-rnaseq/./workflows/../subworkflows/local/prepare_genome/main.nf' at line: 149 or see '.nextflow.log' file for more details

This appears to be due to the following line, in the PREPARE_GENOME module:

ch_versions         = ch_versions.mix(GTF_FILTER.out.versions)

The GTF_FILTER versions is already defined in line 97 of the same script, so I'm not sure it's required again here. Removing this line also appears to resolve the issue.

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 Nov 20, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5e42930

+| ✅ 144 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 3.13.1
  • 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 2.10
  • Run at 2023-11-20 19:04:41

pinin4fjords
pinin4fjords approved these changes Nov 20, 2023
View reviewed changes
Copy link
Member

@pinin4fjords pinin4fjords left a comment

Choose a reason for hiding this comment

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

Looks good- thanks for the fix!

@pinin4fjords
Copy link
Member

@nf-core-bot fix linting

@pinin4fjords pinin4fjords merged commit da99418 into nf-core:dev Nov 20, 2023
16 of 29 checks passed
@pinin4fjords pinin4fjords mentioned this pull request Nov 20, 2023
Closed
@RHReynolds
Copy link
Contributor Author

Thanks for the review!

@RHReynolds RHReynolds deleted the fix-skip-gtf branch November 21, 2023 09:56
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@pinin4fjords pinin4fjords pinin4fjords 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.
4 participants
@RHReynolds @pinin4fjords @rhr-cosyne @nf-core-bot