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Add iptm and ipsae reporting - #592

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JoseEspinosa merged 16 commits into
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add-iptm-ipsae
May 14, 2026
Merged

Add iptm and ipsae reporting#592
JoseEspinosa merged 16 commits into
devfrom
add-iptm-ipsae

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@jscgh

@jscgh jscgh commented Apr 23, 2026 •
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This PR adds interface-metric reporting across supported modes.

  • add iPTM, ipSAE, chainwise iPTM, and chainwise ipSAE TSV outputs where available
  • include iPTM and max ipSAE summary values in HTML reports
  • render chainwise iPTM and ipSAE as chain-by-chain matrices in the HTML report
  • note: interface metrics not supported for ESMFold, RoseTTAFold-All-Atom, and RoseTTAFold2NA

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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.

@jscgh jscgh added this to the 2.1.0 milestone Apr 23, 2026
@jscgh jscgh self-assigned this Apr 23, 2026
@jscgh jscgh added the enhancement Improvement for existing functionality label Apr 23, 2026
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@jscgh jscgh added the WIP Work in progress label Apr 23, 2026
@jscgh
jscgh changed the base branch from master to dev April 23, 2026 07:25
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github-actions Bot commented Apr 24, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit df98899

+| ✅ 349 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  31 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 4.0.2
  • Run at 2026-05-14 09:09:22

@jscgh
jscgh force-pushed the add-iptm-ipsae branch 2 times, most recently from ba861cc to df15821 Compare April 24, 2026 06:44
@keiran-rowell-unsw keiran-rowell-unsw mentioned this pull request Apr 30, 2026
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@keiran-rowell-unsw
keiran-rowell-unsw self-requested a review May 1, 2026 05:01
@keiran-rowell-unsw keiran-rowell-unsw mentioned this pull request May 11, 2026
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@jscgh
jscgh force-pushed the add-iptm-ipsae branch from 0233ac3 to df25edf Compare May 12, 2026 00:05
JoseEspinosa
JoseEspinosa reviewed May 12, 2026
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@JoseEspinosa JoseEspinosa left a comment

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Was trying to fix merge errors. On #601 I updated the plddt files to be named with the suffix _mqc.tsv since otherwise, they are not included in the report. For boltz we will need to also rename the output until the new refactoring for multiqc gets in.

@jscgh
jscgh marked this pull request as ready for review May 13, 2026 06:37
JoseEspinosa
JoseEspinosa approved these changes May 13, 2026
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LGTM! Awesome job! Just small suggestions mainly format issues

Comment thread bin/ipsae.py
Comment thread modules/local/colabfold_batch/main.nf Outdated
Comment thread bin/extract_metrics.py Outdated
Comment thread bin/extract_metrics.py Outdated
Comment thread bin/extract_metrics.py Outdated
rows = [[""] + pair_labels]
for model_idx, score_values in pair_score_entries.items():
score_map = {label: value for label, value in score_values}
rows.append([model_idx] + [f"{score_map.get(label, 0.0):.4f}" for label in pair_labels])

@JoseEspinosa JoseEspinosa May 13, 2026

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Should we populate the default be n/a instead?

@jscgh jscgh May 14, 2026

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Done!

Comment thread modules/local/run_alphafold3/main.nf Outdated
Comment thread modules/local/run_helixfold3/main.nf Outdated
Comment thread modules/local/run_alphafold2_pred/main.nf Outdated
@JoseEspinosa

JoseEspinosa commented May 14, 2026

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Thanks @jscgh! Can we merge it, or should we wait for @keiran-rowell-unsw for a second opinion?

@jscgh jscgh removed the WIP Work in progress label May 14, 2026
@jscgh

jscgh commented May 14, 2026

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Thanks @jscgh! Can we merge it, or should we wait for @keiran-rowell-unsw for a second opinion?

Ready to merge! Sorry, I went to merge before I left the office but I must've shutdown too quickly for it to actually finish the merge.

@JoseEspinosa
JoseEspinosa merged commit c8628b5 into dev May 14, 2026
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@JoseEspinosa
JoseEspinosa deleted the add-iptm-ipsae branch May 14, 2026 09:56
@JoseEspinosa

JoseEspinosa commented May 14, 2026

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No worries! Thanks!

@jscgh jscgh mentioned this pull request May 28, 2026
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes
@keiran-rowell-unsw keiran-rowell-unsw Awaiting requested review from keiran-rowell-unsw

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