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Clean HelixFold3 outputs#461

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jscgh merged 1 commit into
nf-core:devfrom
Australian-Structural-Biology-Computing:clean-hf3-outputs
Feb 11, 2026
Merged

Clean HelixFold3 outputs#461
jscgh merged 1 commit into
nf-core:devfrom
Australian-Structural-Biology-Computing:clean-hf3-outputs

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@jscgh jscgh commented Feb 9, 2026 •
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Group outputs into a raw directory, updating publishing patterns, and ensuring intermediate files are handled correctly.

Addresses the HF3 component of #394

PR checklist

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

@jscgh jscgh added this to the 2.0.0 milestone Feb 9, 2026
@jscgh jscgh self-assigned this Feb 9, 2026
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github-actions Bot commented Feb 9, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c7bd164

+| ✅ 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 2026-02-11 22:56:49

@jscgh jscgh force-pushed the clean-hf3-outputs branch from aaaabea to 0f26244 Compare February 9, 2026 03:06
@jscgh jscgh marked this pull request as ready for review February 9, 2026 03:06
JoseEspinosa
JoseEspinosa approved these changes Feb 11, 2026
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Just a small suggestion and a comment more related to alphafold2 than affecting this PR but otherwise LGTM! 🚀
Also, can not fix myself the conflicts that probably are related to the changelog

Comment thread modules/local/run_helixfold3/main.nf Outdated
Comment thread modules/local/run_helixfold3/main.nf Outdated
@jscgh jscgh force-pushed the clean-hf3-outputs branch from f95285a to c7bd164 Compare February 11, 2026 22:55
@jscgh jscgh merged commit 9722fa0 into nf-core:dev Feb 11, 2026
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@jscgh jscgh deleted the clean-hf3-outputs branch February 11, 2026 23:00
@JoseEspinosa JoseEspinosa mentioned this pull request Mar 18, 2026
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