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Logging to stdout and better errors #186

Merged
merged 10 commits into from Dec 13, 2022
Merged

Logging to stdout and better errors #186

merged 10 commits into from Dec 13, 2022

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ggabernet
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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/epitopeprediction 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 Dec 12, 2022 •
edited

nf-core lint overall result: Failed ❌

Posted for pipeline commit 91f7636

+| ✅ 148 tests passed       |+
!| ❗   2 tests had warnings |!
-| ❌   8 tests failed       |-

❌ Test failures:

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.1
  • Run at 2022-12-13 09:04:04

christopher-mohr
christopher-mohr requested changes Dec 12, 2022
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👍 Some minor comments.

CHANGELOG.md Outdated Show resolved Hide resolved
bin/check_samplesheet.py Outdated Show resolved Hide resolved
bin/check_samplesheet.py Outdated Show resolved Hide resolved
ggabernet and others added 2 commits December 12, 2022 17:01
@ggabernet @christopher-mohr
Update CHANGELOG.md
1aba302 
Co-authored-by: Christopher Mohr <christopher.mohr@uni-tuebingen.de>
@ggabernet
undo changes samplesheet
5324001
christopher-mohr
christopher-mohr approved these changes Dec 12, 2022
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LGTM!

@ggabernet ggabernet merged commit 26ef39f into nf-core:dev Dec 13, 2022
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@christopher-mohr christopher-mohr christopher-mohr approved these changes

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@ggabernet @christopher-mohr