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fix Download Pipeline Workflow #726

Merged
merged 2 commits into from
Mar 28, 2024
Merged

fix Download Pipeline Workflow #726

merged 2 commits into from
Mar 28, 2024

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d4straub
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@d4straub d4straub commented Mar 28, 2024 •
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On release, a test called Test successful pipeline download with 'nf-core download' / download (pull_request) is executed and fails.

There seem to be two reasons:
(1) The pipeline doesnt have in all modules a stub: section, therefore using -stub will fail
(2) There is a problem with downloading the QIIME2 image, see here. This works locally and I do not know why it fails in the test.

Solutions added here:
(1) Implemented nf-core/tools#2846
(2) Added --skip_qiime to remove the need for the QIIME2 container

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/ampliseq 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 Mar 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1c5ea7c

+| ✅ 190 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.9.0
  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-28 12:56:49

mirpedrol
mirpedrol approved these changes Mar 28, 2024
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LGTM

.github/workflows/download_pipeline.yml Outdated Show resolved Hide resolved
.github/workflows/download_pipeline.yml Outdated Show resolved Hide resolved
@d4straub @mirpedrol
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1c5ea7c 
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
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Thanks!

@d4straub d4straub merged commit 3f2f466 into nf-core:dev Mar 28, 2024
17 checks passed
@d4straub d4straub deleted the fix-Download-Pipeline-Workflow branch March 28, 2024 13:42
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