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Add random_seed for AF2, Boltz and ColabFold#588

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jscgh wants to merge 8 commits intodevfrom
add-random_seed
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Add random_seed for AF2, Boltz and ColabFold#588
jscgh wants to merge 8 commits intodevfrom
add-random_seed

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@jscgh jscgh commented Apr 20, 2026 •
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This pull request adds support for explicit random seed control across the alphafold2, boltz, and colabfold modules, improving reproducibility for stochastic inference. Users can now set a global --random_seed parameter, or override it with mode-specific parameters. Documentation and schema files have been updated to reflect these new options.

  • Introduced boltz_random_seed, and colabfold_random_seed parameters in both nextflow.config and nextflow_schema.json. These override the global seed when specified.
  • Added a pipeline-wide random_seed parameter to nextflow.config and nextflow_schema.json, allowing users to set a global seed for all supported modules. Each module now uses its mode-specific seed if provided, otherwise falls back to the global seed (random_seed).

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • CHANGELOG.md is updated.

@jscgh jscgh self-assigned this Apr 20, 2026
@jscgh jscgh added the enhancement Improvement for existing functionality label Apr 20, 2026
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github-actions bot commented Apr 20, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 042dca4

+| ✅ 343 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  30 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 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
  • 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!
  • 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 - prepare_esmfold_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_rosettafold2na_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_boltz_dbs.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_colabfold_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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-04-21 00:20:55

jscgh added 3 commits April 20, 2026 15:35
@jscgh
Update random seed descriptions to emphasise reproducibility
8c1092a
@jscgh
Updated changelog
6916112
@jscgh
Bumped nf-core version to fix bug.
4d66b6b 
Latest version is a tool release.
Template needs to be manually updated to satisfy nf-core-bot
@jscgh jscgh force-pushed the add-random_seed branch from 0c7fab4 to 4d66b6b Compare April 20, 2026 05:36
@jscgh jscgh marked this pull request as draft April 20, 2026 05:40
@jscgh jscgh force-pushed the add-random_seed branch from dbf3138 to 59b5ec0 Compare April 20, 2026 06:00
@jscgh jscgh marked this pull request as ready for review April 20, 2026 06:00
tlitfin
tlitfin reviewed Apr 20, 2026
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Comment thread conf/modules_alphafold2.config Outdated
tlitfin
tlitfin reviewed Apr 20, 2026
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Comment thread docs/usage.md
tlitfin
tlitfin requested changes Apr 20, 2026
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I have requested minor changes.

I am also a bit conflicted about whether it is best to:
a) Only support mode-specific flags (so there is no confusion if using the global flag for a non-supported mode). We do expose max-template-date as a mode specific flag only which is a similar precedent.
b) Only support global flag (to avoid creating many additional pipeline params since users will never want to set different mode-level seeds).
c) Current behaviour with global flag (for convenience) + mode-specific flags. Do the mode specific flags add value here?

My gut feel is a slight preference for b > a > c. Not sure if others have a strong opinion here.

We should probably review the way we define these shared parameters to make sure they are consistent (eg max-template-date - although this can probably be deprecated as a pipeline parameter and hard-coded to future date in ext.args).

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