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Enlarge the sampling range for column determination in FilterGTF script. #1127

Merged
merged 4 commits into from
Nov 20, 2023
Merged

Enlarge the sampling range for column determination in FilterGTF script. #1127

merged 4 commits into from
Nov 20, 2023

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MatthiasZepper
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Large, multi-line comments at the top of GTF files disrupt the function to determine the number of columns in filter_gtf.py, therefore the sampling range was increased hundredfold to avoid erroneously rejecting a valid file.

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 Nov 20, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9250c4c

+| ✅ 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 21:05:46

pinin4fjords
pinin4fjords approved these changes Nov 20, 2023
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LGTM- thanks for the fix!

@pinin4fjords pinin4fjords merged commit 76464e4 into nf-core:dev Nov 20, 2023
14 of 29 checks passed
@MatthiasZepper MatthiasZepper deleted the FilterGTF_enlage_sample branch January 9, 2024 11:13
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

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@MatthiasZepper @pinin4fjords