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Added Busco to run in protein mode #142

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Added Busco to run in protein mode #142

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SandraBabirye
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@SandraBabirye SandraBabirye commented Sep 18, 2024 •
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PR checklist

  • Edited the annotation_statistics subworkflow: added the gffread nfcore module to obtain the protein.fasta file and hard coded the busco to run in protein mode
  • Edited the extract annotatistics local module bby adding a new input channel for the Busco statistics
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

@SandraBabirye
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SandraBabirye commented Sep 18, 2024 •
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Hi @BethYates and @tkchafin , Kindly review my commits towards solving issue 141. Thank you

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github-actions bot commented Sep 18, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7fe58fc

+| ✅ 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 2024-09-23 10:02:07

@BethYates
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We need to pass an argument -y to the GFFREAD process to tell it to output protein fasta sequences, to do this you need to add the following to the process block in modules.config
withName: GFFREAD { ext.args = "-y" }

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@SandraBabirye @BethYates