8000 Deactivate saving of reads and other large files for full tests by jfy133 · Pull Request #269 · nf-core/taxprofiler · GitHub
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Deactivate saving of reads and other large files for full tests #269

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Merged
merged 2 commits into from
Mar 17, 2023
Merged

Deactivate saving of reads and other large files for full tests #269

merged 2 commits into from
Mar 17, 2023

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jfy133
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@jfy133 jfy133 commented Mar 17, 2023 •
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Re: https://nfcore.slack.com/archives/CTY8L26C8/p1679040181299829?thread_ts=1678923529.023299&cid=CTY8L26C8 and https://nfcore.slack.com/archives/DEL52B0U8/p1679040013345729

Hopefully if I can get it to work, in teh future we can have a system to save the final reads that go into preprocessing a la the diea at the bottom fo #262, and save only those

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/taxprofiler 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).

@jfy133 jfy133 requested a review from a team March 17, 2023 09:19
sofstam
sofstam reviewed Mar 17, 2023
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conf/test_full.config

perform_shortread_qc = true
shortread_qc_mergepairs = true
perform_shortread_complexityfilter = false
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Shall we also deactivate this flag?

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Oh oops! I got overzealosu

jfy133
jfy133 commented Mar 17, 2023
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conf/test_full.config

perform_shortread_qc = true
shortread_qc_mergepairs = true
perform_shortread_complexityfilter = false
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Suggested change
perform_shortread_complexityfilter = false
perform_shortread_complexityfilter = true

jfy133
jfy133 commented Mar 17, 2023
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jfy133
jfy133 commented Mar 17, 2023
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github-actions bot commented Mar 17, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 142ff2f

+| ✅ 156 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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
  • schema_lint - Schema 'description' should be 'Taxonomic classification and profiling of shotgun metagenomic data'
    Found: 'Taxonomic profiling of shotgun metagenomic data'

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-17 09:28:32

@sofstam sofstam self-requested a review March 17, 2023 09:32
@jfy133 jfy133 merged commit af61e00 into dev Mar 17, 2023
@jfy133 jfy133 deleted the reduce-full-test-output branch March 17, 2023 10:46
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@Midnighter Midnighter Midnighter approved these changes

@sofstam sofstam sofstam approved these changes

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