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skip haplocheck and fastqc [skip ci] #438

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Merged
merged 4 commits into from
Oct 26, 2023
Merged

skip haplocheck and fastqc [skip ci] #438

merged 4 commits into from
Oct 26, 2023

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@ramprasadn
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@ramprasadn ramprasadn commented Oct 26, 2023 •
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PR checklist

Add parameters to skip fastqc and haplocheck

  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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 Oct 26, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a88a83b

+| ✅ 151 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-26 14:11:02

@ramprasadn ramprasadn marked this pull request as ready for review October 26, 2023 12:28
@ramprasadn ramprasadn requested a review from jemten October 26, 2023 12:28
jemten
jemten approved these changes Oct 26, 2023
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It's unfortunate that this is necessary in order to pass CI on github actions. We should start looking into the nf-test once that is a little less beta

@ramprasadn ramprasadn merged commit 4ca4db2 into nf-core:dev Oct 26, 2023
@ramprasadn ramprasadn deleted the skip-modules branch February 2, 2024 16:57
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@jemten jemten jemten approved these changes

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@ramprasadn @jemten