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Merged
merged 5 commits into from
Jul 20, 2023
Merged

Add QC check for empty files out of annotation #297

merged 5 commits into from
Jul 20, 2023

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jfy133
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@jfy133 jfy133 commented Jul 19, 2023

closes #246

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/funcscan 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).

@jfy133 jfy133 changed the base branch from master to dev July 19, 2023 08:45
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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 @jfy133,

It looks like this pull-request is has been made against the nf-core/funcscan 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 nf-core/funcscan 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!

jfy133
jfy133 commented Jul 19, 2023
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@jfy133 jfy133 changed the title Start qc Add QC check for empty files out of annotation Jul 19, 2023
@jfy133 jfy133 requested a review from a team July 19, 2023 08:46
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github-actions bot commented Jul 19, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9d16c0d

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • 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 passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-20 07:39:21

louperelo
louperelo approved these changes Jul 19, 2023
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Looks good to me.

@jfy133 jfy133 merged commit 2a5c3ee into dev Jul 20, 2023
@jfy133 jfy133 deleted the start-qc branch July 20, 2023 09:08
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@louperelo louperelo louperelo approved these changes

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Add QC check after annotation to avoid empty annotation files being screened
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@jfy133 @louperelo