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More checks of sample-sheet #629

Merged
merged 5 commits into from
Jul 12, 2022
Merged

More checks of sample-sheet #629

merged 5 commits into from
Jul 12, 2022

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asp8200
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@asp8200 asp8200 commented Jul 12, 2022 •
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Two checks for ensuring that the pipeline stops with a meaningful error message if

  1. the sample-sheet only contains normal-samples, but some of the requested tools require tumor-samples, and
  2. the sample-sheet only contains tumor-samples, but some of the requested tools require normal-samples.

I did some test-runs of the this with sample-sheet containing

  1. only normal-samples,
  2. only tumor-samples, and
  3. a mix of normal samples and tumor-samples.

@lassefolkersen might also do some test-runs for these new checks.

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • 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 Jul 12, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a3b769c

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_description - No description provided in schema for parameter: ascat_chromosomes

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-12 18:06:53

maxulysse
maxulysse reviewed Jul 12, 2022
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maxulysse
maxulysse reviewed Jul 12, 2022
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@asp8200 asp8200 changed the title DRAFT: More checks of sample-sheet More checks of sample-sheet Jul 12, 2022
@asp8200 asp8200 marked this pull request as ready for review July 12, 2022 14:13
@asp8200 asp8200 requested a review from maxulysse July 12, 2022 14:15
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Can you update the CHANGELOG?

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asp8200 commented Jul 12, 2022

Can you update the CHANGELOG?

A shot! I always forget

maxulysse
maxulysse reviewed Jul 12, 2022
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@asp8200 @maxulysse
Update workflows/sarek.nf
f0e361d 
shorter variable names

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
@asp8200 asp8200 requested a review from maxulysse July 12, 2022 18:05
@maxulysse maxulysse merged commit 7877e77 into nf-core:dev Jul 12, 2022
@asp8200 asp8200 mentioned this pull request Jul 13, 2022
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@lassefolkersen lassefolkersen Awaiting requested review from lassefolkersen

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@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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