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Move fasta check back to Groovy #1143

Merged
merged 9 commits into from
Jan 3, 2024
Merged

Move fasta check back to Groovy #1143

merged 9 commits into from
Jan 3, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Dec 21, 2023 •
edited

Closes #1142

Ideally we would validate at the schema, but this won't work unless nf-core/tools#2619 resolves quickly.

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).

@pinin4fjords pinin4fjords linked an issue Dec 21, 2023 that may be closed by this pull request
'fasta' should not be required if --genome supplied #1142
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github-actions bot commented Jan 3, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8d7edfb

+| ✅ 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 18:14:50

@pinin4fjords pinin4fjords changed the title Try more flexible requires for genome Move fasta check back to Groovy Jan 3, 2024
drpatelh
drpatelh approved these changes Jan 3, 2024
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@drpatelh drpatelh mentioned this pull request Jan 3, 2024
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@drpatelh drpatelh merged commit 221bdca into dev Jan 3, 2024
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@drpatelh drpatelh mentioned this pull request Jan 4, 2024
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@drpatelh drpatelh deleted the genome_fasta_required branch January 21, 2024 09:38
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'fasta' should not be required if --genome supplied
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