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update confs - dev and pride ebi #443

Merged
merged 4 commits into from
Nov 24, 2024
Merged

update confs - dev and pride ebi #443

merged 4 commits into from
Nov 24, 2024
+2 −2

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ypriverol
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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/quantms 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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coderabbitai bot commented Nov 24, 2024

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github-actions bot commented Nov 24, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0d79049

+| ✅ 108 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗  11 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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 ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-24 20:10:04

@ypriverol ypriverol merged commit 0a8d513 into bigbio:dev Nov 24, 2024
20 checks passed
jpfeuffer
jpfeuffer reviewed Nov 24, 2024
View reviewed changes
conf/pride_codon_slurm.config
@@ -27,7 +27,7 @@ singularity {
process {
// this is to avoid errors for missing files due to shared filesystem latency
maxRetries = 30
errorStrategy = { task.exitStatus == 0 ? "retry" : "terminate" }
errorStrategy = { task.exitStatus in ((130..145) + 104 + 1 + 9 + 134 + 97 + 137 + 0) ? "retry" : "terminate" }
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That looks quite redundant 134 and 137 are between (130..145) 😄 and retry for status 0? Doesn't status 0 mean successful?

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Got it.

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