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Add GPU actions workflow and RUN_BOLTZ module test.#632

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gpu-actions-workflow
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Add GPU actions workflow and RUN_BOLTZ module test.#632
tlitfin wants to merge 15 commits into
devfrom
gpu-actions-workflow

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@tlitfin

@tlitfin tlitfin commented May 31, 2026 •
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  • Added a gpu github actions workflow based on the example in nf-core/rnaseq.
    • Chose g5 instance instead of g4dn for bfloat16 compatibility.
    • Temporarily requires manual trigger until confirming use of GPU runners is OK (@JoseEspinosa).
  • Added a RUN_BOLTZ gpu module test.
    • GPU inference likely not 100% deterministic even with seed set so only checked for success (not snapshot).
    • Temporarily disabled due to not engaging GPU on runners.
  • Added a COLABFOLD_BATCH gpu module test.
  • Temporarily pointing at my test-data repo (similar to Add cpu module tests for boltz workflow #631).

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>).
  • 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 995c6fd

+| ✅ 352 tests passed       |+
#| ❔   4 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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
  • 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 - prepare_alphafold2_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_esmfold_dbs.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_alphafold3_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 - aria2_uncompress.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
  • local_component_structure - prepare_boltz_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-31 12:17:41

@tlitfin tlitfin force-pushed the gpu-actions-workflow branch 2 times, most recently from 640728e to 0a18a8e Compare May 31, 2026 07:17
@tlitfin tlitfin force-pushed the gpu-actions-workflow branch from 0a18a8e to 9d63c3f Compare May 31, 2026 07:30
@tlitfin

tlitfin commented May 31, 2026

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I killed GPU test on runner because it took much longer than it should. I suspect it is not correctly engaging the GPU. Will have to troubleshoot.

@tlitfin tlitfin force-pushed the gpu-actions-workflow branch 2 times, most recently from 665fa61 to 48b7f65 Compare May 31, 2026 12:10
@tlitfin tlitfin force-pushed the gpu-actions-workflow branch from 48b7f65 to 995c6fd Compare May 31, 2026 12:16
@tlitfin

tlitfin commented May 31, 2026

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Added a colabfold_batch gpu test which works correctly. May be something specific to Boltz image re: nvidia driver or similar.

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