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Update publishdir patterns for alphafold2 modules#454

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JoseEspinosa merged 4 commits into
nf-core:devfrom
tlitfin:clean-af2-outputs
Feb 5, 2026
Merged

Update publishdir patterns for alphafold2 modules#454
JoseEspinosa merged 4 commits into
nf-core:devfrom
tlitfin:clean-af2-outputs

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@tlitfin tlitfin commented Jan 29, 2026 •
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Closes #393

Addresses the AlphaFold2 component of #394 as a potential template for other modes. I do like the idea of more fine-grained control of outputs as proposed in #453 but maybe can wait until future release? Probably need some balance between amount of control and a large number of parameters.

Have tested with monomer and multimer in split_msa and standard modes.

I went with the following structure where publishing 'raw' intermediate data is gated by --keep_raw parameter (false by default).

output/alphafold2/
└── standard
    ├── test-dimer
    │   ├── paes [25 entries exceeds filelimit, not opening dir]
    │   ├── raw [182 entries exceeds filelimit, not opening dir]  <-- raw output data in here
    │   ├── test-dimer_alphafold2_msa.tsv
    │   ├── test-dimer_iptm.tsv
    │   ├── test-dimer_plddt.tsv
    │   └── test-dimer_ptm.tsv
    └── top_ranked_structures
        └── test-dimer.pdb

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • CHANGELOG.md is updated.

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github-actions Bot commented Jan 29, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit caf62a9

+| ✅ 328 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  33 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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!
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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 - post_processing.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_rosettafold2na_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_colabfold_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_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_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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-02-04 23:40:53

@tlitfin tlitfin marked this pull request as ready for review January 29, 2026 22:25
@tlitfin tlitfin mentioned this pull request Jan 30, 2026
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JoseEspinosa
JoseEspinosa requested changes Feb 4, 2026
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Just a couple of small suggestions but very nice and clean!

Comment thread conf/modules_alphafold2.config Outdated
Comment thread conf/modules_alphafold2.config Outdated
Comment thread modules/local/run_alphafold2/main.nf
Comment thread nextflow.config Outdated
Comment thread nextflow_schema.json Outdated
Comment thread conf/modules_alphafold2.config Outdated
Comment thread conf/modules_alphafold2.config Outdated
Comment thread nextflow.config Outdated
Comment thread nextflow_schema.json Outdated
JoseEspinosa
JoseEspinosa approved these changes Feb 5, 2026
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Awesome 🚀 Thanks!

@JoseEspinosa JoseEspinosa merged commit 99d65e2 into nf-core:dev Feb 5, 2026
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@keiran-rowell-unsw keiran-rowell-unsw mentioned this pull request Feb 11, 2026
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@JoseEspinosa JoseEspinosa mentioned this pull request Mar 18, 2026
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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