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Temporary test full profile (until container and tax anno reference files fixed) #575

Merged
merged 9 commits into from
Feb 5, 2024
Merged

Temporary test full profile (until container and tax anno reference files fixed) #575

merged 9 commits into from
Feb 5, 2024

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jfy133
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@jfy133 jfy133 commented Feb 2, 2024 •
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Context:

  • metaspades container has something that doesn't play well with seqera's fusion FS
  • centrifuge and gtdb database unpacking modules also break for some reason on Aws

Former we need to try different container possibly, latter we apparently need to minimise the amount of file moving operations (or something along those lines... Both Jordi and Adam have looked into these at various points)

So deactivating all of the above for now

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 Feb 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 818b9b4

+| ✅ 211 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 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 WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-05 07:44:09

jfy133
jfy133 commented Feb 4, 2024
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d4straub
d4straub approved these changes Feb 5, 2024
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jfy133
jfy133 commented Feb 5, 2024
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jfy133
jfy133 commented Feb 5, 2024
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@jfy133 jfy133 merged commit fe35d60 into dev Feb 5, 2024
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@jfy133 jfy133 deleted the temp-test-full-profile branch February 5, 2024 07:42
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@d4straub d4straub d4straub approved these changes

@CarsonJM CarsonJM Awaiting requested review from CarsonJM

@maxibor maxibor Awaiting requested review from maxibor

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@jfy133 @d4straub