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Add def for print_error function #145

Merged
merged 1 commit into from Sep 22, 2022
Merged

Add def for print_error function #145

merged 1 commit into from Sep 22, 2022

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vjmarteau
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@vjmarteau vjmarteau commented Sep 22, 2022 •
edited

Print_error() is currently not defined in the check_samplesheet.py script which leads to an error when the Samplesheet does not pass the checks. Copied the function def from the nf-core/rnaseq pipeline.

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/scrnaseq 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 Sep 22, 2022 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 66d2e2f

+| ✅ 153 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • schema_lint - Schema 'description' should be 'Pipeline for processing 10x Genomics single cell rnaseq data'
    Found: 'Pipeline for processing of 10xGenomics single cell rnaseq data'

✅ Tests passed:

Run details

  • nf-core/tools version 2.5.1
  • Run at 2022-09-22 09:38:13

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@nf-core-bot fix linting

apeltzer
apeltzer approved these changes Sep 22, 2022
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Just the linting fix missing, otherwise good 👍🏻

@apeltzer apeltzer merged commit 124f497 into nf-core:dev Sep 22, 2022
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Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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@apeltzer apeltzer apeltzer approved these changes

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@vjmarteau @apeltzer