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Merged
maxulysse merged 17 commits into from
May 27, 2024
Merged

Adding gvcf #138

maxulysse merged 17 commits into from
May 27, 2024

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@maxulysse
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@maxulysse maxulysse commented Apr 4, 2024

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/rnavar 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).

@maxulysse maxulysse changed the base branch from master to dev April 4, 2024 12:18
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github-actions bot commented Apr 4, 2024

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @maxulysse,

It looks like this pull-request is has been made against the maxulysse/nf-core_rnavar master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the maxulysse/nf-core_rnavar dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented Apr 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 66a151a

+| ✅ 202 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowRnavar.groovy: Optionally add in-text citation tools to this list.
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/WorkflowRnavar.groovy
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-rnavar_logo_light.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-27 15:37:02

@maxulysse maxulysse mentioned this pull request May 27, 2024
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maxulysse
maxulysse commented May 27, 2024
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nictru
nictru approved these changes May 27, 2024
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LGTM

@maxulysse maxulysse merged commit a833135 into nf-core:dev May 27, 2024
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@nictru nictru nictru approved these changes

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@maxulysse @nictru @MathieuCharlesINRAE