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Split extract metrics for Colabfold#552

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jscgh wants to merge 33 commits into
nf-core:hackathon_march_2026from
Australian-Structural-Biology-Computing:split-extract_metrics-colabfold
Draft

Split extract metrics for Colabfold#552
jscgh wants to merge 33 commits into
nf-core:hackathon_march_2026from
Australian-Structural-Biology-Computing:split-extract_metrics-colabfold

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@jscgh jscgh commented Mar 13, 2026 •
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Splits extract metrics from Colabfold module.
Closes #545

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 self-assigned this Mar 13, 2026
@jscgh jscgh added the enhancement Improvement for existing functionality label Mar 13, 2026
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github-actions Bot commented Mar 13, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0f72a67

+| ✅ 341 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  32 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - Config manifest.version should end in dev: 2.0.0
  • 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 nextflow.config: Specify any additional parameters here
  • 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 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 - 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_alphafold3_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_alphafold2_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 - aria2_uncompress.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_boltz_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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-18 05:37:47

@jscgh jscgh marked this pull request as ready for review March 13, 2026 04:04
@JoseEspinosa
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JoseEspinosa commented Mar 13, 2026

Sorry I think I introduced the conflicts and have not access to this branch to fix them 😢

@jscgh jscgh requested a review from JoseEspinosa March 14, 2026 03:00
@jscgh jscgh force-pushed the split-extract_metrics-colabfold branch from b83229b to 4957381 Compare March 14, 2026 03:09
@jscgh jscgh linked an issue Mar 14, 2026 that may be closed by this pull request
Split EXTRACT_METRICS for ColabFold #545
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@jscgh jscgh moved this to Ready for review in Hackathon March 2026 Mar 14, 2026
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jscgh commented Mar 14, 2026 •
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Sorry I think I introduced the conflicts and have not access to this branch to fix them 😢

Whoops, didn't mean to push this to the other repo. I've rebased the branch and given you permissions to write in case it diverges again.

@jscgh jscgh marked this pull request as draft March 16, 2026 11:17
@JoseEspinosa
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JoseEspinosa commented Mar 16, 2026

I can't still fix the conflicts, sorry 😢

@jscgh jscgh force-pushed the split-extract_metrics-colabfold branch from 4957381 to 80bbfc1 Compare March 18, 2026 05:18
@jscgh jscgh marked this pull request as ready for review March 18, 2026 05:53
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jscgh commented Mar 18, 2026

I can't still fix the conflicts, sorry 😢

I had to import the updated test configs and update snapshots. Everything looks green now.

@jscgh jscgh force-pushed the hackathon_march_2026 branch from 484b1b8 to 2057b9d Compare April 16, 2026 06:08
@jscgh jscgh marked this pull request as draft April 16, 2026 23:58
@jscgh jscgh added WIP Work in progress and removed Ready for review labels Apr 16, 2026
@jscgh jscgh added this to the 3.0.0 milestone Apr 23, 2026
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Reviewers

@JoseEspinosa JoseEspinosa Awaiting requested review from JoseEspinosa

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@jscgh jscgh

Labels

enhancement Improvement for existing functionality WIP Work in progress

Projects

Hackathon March 2026
Status: Ready for review

Milestone

3.0.0

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Successfully merging this pull request may close these issues.

Split EXTRACT_METRICS for ColabFold

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@jscgh @JoseEspinosa @sblaizerwize @tlitfin