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Preserve STDERR #1345

Merged
merged 8 commits into from
Dec 8, 2023
Merged

Preserve STDERR #1345

merged 8 commits into from
Dec 8, 2023

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sminot
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@sminot sminot commented Nov 30, 2023

I ran into an error which was very hard to debug because I couldn't see the contents of STDERR.

This should preserve STDERR in the logs without altering the set of files which are written out.

PR checklist

  • [ x ] 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/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 --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 Nov 30, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4ca5499

+| ✅ 144 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • 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
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-08 11:08:51

@maxulysse
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cf nf-core/modules#4520

This was referenced Dec 8, 2023
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@maxulysse maxulysse merged commit ccac395 into nf-core:dev Dec 8, 2023
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@sminot sminot deleted the preserve_stderr branch December 8, 2023 15:14
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@maxulysse maxulysse maxulysse approved these changes

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@sminot @maxulysse @FriederikeHanssen