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Add cpu module tests for boltz workflow#631

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tlitfin wants to merge 7 commits into
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module-tests
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Add cpu module tests for boltz workflow#631
tlitfin wants to merge 7 commits into
devfrom
module-tests

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@tlitfin

@tlitfin tlitfin commented May 31, 2026 •
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Following up from #621, there were many edge cases which could cause errors in the future (eg colabfold_search does not maintain the ordering of entities which can break PTMs and contact constraints if not handled carefully). This PR adds several module tests to avoid breaking edge cases in future development. Tests for the following modules are added.

Very lightweight:

  • boltz_fasta: convert fasta input to boltz yaml (with tagged or automatic entity type assignment)
  • boltz_yaml_to_colabfold_fasta: convert boltz yaml format to colabfold fasta
  • split_msa: convert af3 json format (with msas) to boltz yaml using with entity order and additional metadata derived from original boltz yaml (without msas).

Less lightweight:

  • mmseqs_colabfoldsearch: construct msa by searching colabfold database. Could make this more lightweight by further trimming uniref30 db. Should add multimer test when upstream bug fixed or mapping available for uniref30 minidb.

Note: This is pointing at my test-data fork. Can submit PR to add test data to nf-core after PR is approved.

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 necessary, also make a PR on the nf-core/proteinfold 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>).
  • CHANGELOG.md is updated.

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github-actions Bot commented May 31, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eb68fd1

+| ✅ 351 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  31 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_description - No description provided in schema for parameter: rosettafold2na_uniref30_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_bfd_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_pdb100_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_weights_link
  • schema_description - No description provided in schema for parameter: rfam_full_region_link
  • schema_description - No description provided in schema for parameter: rfam_cm_link
  • schema_description - No description provided in schema for parameter: rnacentral_rfam_annotations_link
  • schema_description - No description provided in schema for parameter: rnacentral_id_mapping_link
  • schema_description - No description provided in schema for parameter: rnacentral_sequences_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_uniref30_path
  • schema_description - No description provided in schema for parameter: rosettafold2na_bfd_path
  • schema_description - No description provided in schema for parameter: rosettafold2na_pdb100_path
  • schema_description - No description provided in schema for parameter: rosettafold2na_weights_path
  • local_component_structure - aria2_uncompress.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - post_processing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_alphafold2_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_esmfold_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_rosettafold_all_atom_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_alphafold3_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_rosettafold2na_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_boltz_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_colabfold_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_helixfold3_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-19 00:25:46

@tlitfin tlitfin added this to the 2.1.0 milestone May 31, 2026
@tlitfin tlitfin mentioned this pull request May 31, 2026
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jscgh
jscgh approved these changes Jun 19, 2026
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@jscgh jscgh left a comment •
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Looks good to me and passed all my tests. As well as updating the test data it would be good to update the colabfold_uniref30 minidbs with the micro version.

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