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Fix handling of BUSCO output with auto lineage selection #226

Merged
merged 2 commits into from
Jul 28, 2021
Merged

Fix handling of BUSCO output with auto lineage selection #226

merged 2 commits into from
Jul 28, 2021

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skrakau
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@skrakau skrakau commented Jul 28, 2021 •
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Fix handling of BUSCO output with auto lineage selection for the case that both domain and specific linear could be selected successfully, i.e. without error or problems due to missing marker genes, and that the specific lineage is still the same as the generic one. In this case there is no short_summary.generic.* file produced by BUSCO.

-> used results for specific lineage also for domain. Thus, in this case, the lineage bacteria_odb10 would be listed as specific lineage dataset and only when the specific lineage could not be selected (i.e. BUSCO errors occur) due to failed placements the results for the specific lineage dataset would be NA.

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md)
    • 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).
  • 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 Jul 28, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c5cd2f7

+| ✅ 135 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '2.1.0'
  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-07-28 11:25:53

@skrakau skrakau requested a review from d4straub July 28, 2021 11:28
@skrakau skrakau marked this pull request as ready for review July 28, 2021 11:29
d4straub
d4straub approved these changes Jul 28, 2021
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Looks good!

@skrakau skrakau merged commit 2fecf1f into nf-core:dev Jul 28, 2021
@skrakau skrakau deleted the fix_busco_issue branch July 22, 2022 09:21
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@d4straub d4straub d4straub approved these changes

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