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Jessicarowell/add blast blastp #41

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@jessicarowell jessicarowell commented May 13, 2025 •
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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/proteinannotator branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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).

@jessicarowell jessicarowell requested a review from olgabot May 13, 2025 21:10
@jessicarowell jessicarowell self-assigned this May 13, 2025
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github-actions bot commented May 14, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit d33da85

+| ✅ 180 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   3 tests had warnings |!
-| ❌   2 tests failed       |-
Details

❌ Test failures:

  • schema_params - Param blast_ref_fasta from nextflow config not found in nextflow_schema.json
  • schema_params - Param blastp_outfmt from nextflow config not found in nextflow_schema.json

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/ci.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-proteinannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_dark.png
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-05-14 21:25:34

@jessicarowell jessicarowell changed the title WIP - Jessicarowell/add blast blastp Jessicarowell/add blast blastp May 14, 2025
olgabot
olgabot requested changes May 16, 2025
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Hello! Thank you so much for your hard work. Please make sure to add to the output documentation (docs/ folder), add your tool to the README.md list, USAGE.md as well.

Check out the rnaseq pipeline docs for inspiration:

If you feel so inclined, feel free to update the lines from orange to green on the BLASTP metromap using the VS Code Excalidraw extension!

Thank you so much!

subworkflows/local/functional_annotation/main.nf
// SUBWORKFLOW: BLASTP
//
BLASTP (
ch_multifasta, params.blastp_outfmt
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Suggested change
ch_multifasta, params.blastp_outfmt
ch_multifasta,
params.blastp_outfmt

Add 4 space indentation and parameters on separate lines for readability

subworkflows/local/functional_annotation/main.nf
ch_multifasta, params.blastp_outfmt
)
ch_versions = ch_versions.mix(BLASTP.out.versions.first())

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Please add the BLASTP output to the pipeline output

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