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Update warning about additional_fasta and gene BED #1038

Merged
merged 3 commits into from
Jun 1, 2023
Merged

Update warning about additional_fasta and gene BED #1038

merged 3 commits into from
Jun 1, 2023

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adamrtalbot
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Based on #1001

  • Update warning based when using --additional_fasta and --gene_bed.

Example of warning:

image

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 Jun 1, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 73eae67

+| ✅ 150 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   3 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 prefered methods description, e.g. add publication citation for this pipeline

❔ 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/NfcoreSchema.groovy
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-01 12:28:48

drpatelh
drpatelh approved these changes Jun 1, 2023
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LGTM!

@drpatelh drpatelh merged commit ef8022e into nf-core:dev Jun 1, 2023
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@drpatelh drpatelh mentioned this pull request Jun 1, 2023
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@drpatelh drpatelh drpatelh approved these changes

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