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Clean alphafold3 outputs#468

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JoseEspinosa merged 15 commits into
nf-core:devfrom
JoseEspinosa:outputs
Feb 12, 2026
Merged

Clean alphafold3 outputs#468
JoseEspinosa merged 15 commits into
nf-core:devfrom
JoseEspinosa:outputs

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@JoseEspinosa JoseEspinosa commented Feb 11, 2026 •
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Group outputs into a raw directory, updating publishing patterns, and ensuring intermediate files are handled correctly.

Addresses the Alphafold3 component of #394

Also, updates nf-test snapshots after #469

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github-actions Bot commented Feb 11, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 442f577

+| ✅ 329 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 2026-02-12 11:25:00

@JoseEspinosa JoseEspinosa marked this pull request as ready for review February 12, 2026 10:39
@JoseEspinosa JoseEspinosa mentioned this pull request Feb 12, 2026
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vagkaratzas
vagkaratzas requested changes Feb 12, 2026
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Nice! Left some comments. You will probably have to update the output.md with the new output structure format, and the CHANGELOG.md as well :D

Comment thread modules/local/run_alphafold3/main.nf Outdated
Comment thread modules/local/run_alphafold3/main.nf
Comment thread modules/local/run_alphafold3/main.nf
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442f577 
Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
vagkaratzas
vagkaratzas approved these changes Feb 12, 2026
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LGTM!

@JoseEspinosa JoseEspinosa merged commit ed8e7a4 into nf-core:dev Feb 12, 2026
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@JoseEspinosa JoseEspinosa mentioned this pull request Mar 18, 2026
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@vagkaratzas vagkaratzas vagkaratzas approved these changes

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@JoseEspinosa @vagkaratzas