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Test count #141

Merged
merged 29 commits into from
May 29, 2024
Merged

Test count #141

merged 29 commits into from
May 29, 2024

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LaurenceKuhl
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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/crisprseq 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 May 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit af1cbe4

+| ✅ 222 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.2.0
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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

❔ Tests ignored:

  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-28 16:09:33

LaurenceKuhl
LaurenceKuhl commented May 27, 2024
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conf/test_screening_count_table.config Outdated Show resolved Hide resolved
conf/test_screening_count_table.config Outdated Show resolved Hide resolved
mirpedrol
mirpedrol reviewed May 27, 2024
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Apart from a couple of last comments, it's looking good!

.github/workflows/download_pipeline.yml Outdated
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I think the changes on this file come from the template update, the previous versions are the correct ones, the most recent.

conf/test_screening_count_table.config Outdated Show resolved Hide resolved
subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf Outdated Show resolved Hide resolved
subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf Outdated Show resolved Hide resolved
@LaurenceKuhl
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hi @mirpedrol i added the if statement again in the pipeline validation otherwise it failed :/

mirpedrol
mirpedrol approved these changes May 28, 2024
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LGTM if my change didn't break the tests :)

@LaurenceKuhl LaurenceKuhl merged commit 7ff5a04 into nf-core:dev May 29, 2024
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@mirpedrol mirpedrol mirpedrol approved these changes

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@LaurenceKuhl @mirpedrol