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Add exit code 12 to SPAdes and standardise custom errorStragety formats #676

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merged 2 commits into from
Sep 24, 2024
Merged

Add exit code 12 to SPAdes and standardise custom errorStragety formats #676

merged 2 commits into from
Sep 24, 2024

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jfy133
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@jfy133 jfy133 commented Sep 23, 2024

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/mag 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 23, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 868cec1

+| ✅ 306 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-24 09:09:22

@jfy133 jfy133 linked an issue Sep 23, 2024 that may be closed by this pull request
SPADES with exit code 12 when running out of memory #675
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@jfy133 jfy133 mentioned this pull request Sep 23, 2024
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d4straub
d4straub approved these changes Sep 24, 2024
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LGTM

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@jfy133 @d4straub
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868cec1 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
@jfy133 jfy133 merged commit f7865e5 into dev Sep 24, 2024
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@jfy133 jfy133 mentioned this pull request Oct 2, 2024
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@jfy133 jfy133 deleted the spades-ec-12 branch October 4, 2024 07:35
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@d4straub d4straub d4straub approved these changes

@prototaxites prototaxites Awaiting requested review from prototaxites

@CarsonJM CarsonJM Awaiting requested review from CarsonJM

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SPADES with exit code 12 when running out of memory
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