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Allow running of metatdata subworkflow on different biosample types #132

Merged
merged 3 commits into from
Jul 30, 2024
Merged

Allow running of metatdata subworkflow on different biosample types #132

merged 3 commits into from
Jul 30, 2024

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reichan1998
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Fixes #114

  • Renamed params.biosample to params.biosample_wgs for the biosample used to produce the genomic sequence.
  • Added params.biosample_hic and params.biosample_rna for the biosample used to produce the HiC data and the biosample used to produce the RNASeq data, respectively.
  • Modified output file to contain information from the biosample data type and then used it to prefix the parameter names in the output file, e.g COLLECTOR would become either "COLLECTOR" or "HIC_COLLECTOR" or "RNA_COLLECTOR".

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
  • 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).

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github-actions bot commented Jul 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e0e8c07

+| ✅ 131 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File does not exist: assets/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomenote/genomenote/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-07-30 05:31:39

@reichan1998 reichan1998 linked an issue Jul 30, 2024 that may be closed by this pull request
Allow running of metatdata subworkflow on multiple specimen IDs #114
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BethYates
BethYates approved these changes Jul 30, 2024
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These changes look great @reichan1998 and give the output desired - thanks!

@BethYates BethYates merged commit 8acc0a0 into sanger-tol:public_dev Jul 30, 2024
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@BethYates BethYates BethYates approved these changes

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Allow running of metatdata subworkflow on multiple specimen IDs
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@reichan1998 @BethYates