nf-core/proteinfold

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Protein 3D structure prediction pipeline

Stars: 115
Forks: 75
Open beginner issues: 0
Indexed issues: 87

Dominant language: HTML
License: MIT
Last GitHub push: Jul 28, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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87 open issues indexed

Lightweight container to avoid pip installing MultiQC Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/proteinfold#654 · Opened Sep 17, 2026
config parsing failed Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

nf-core/proteinfold#650 · 1 comment · Opened Aug 31, 2026
AlphaFold3 data pipeline never finds the Rfam database (Rfam-*.fasta glob does not match the shipped filename) Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

nf-core/proteinfold#649 · Opened Aug 28, 2026
BOLTZ_FASTA errors on more than 62 fasta entries Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 68/100

nf-core/proteinfold#637 · Opened Jun 26, 2026
Downstream mmcif analysis Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/proteinfold#635 · 1 comment · 1 reaction · Opened Jun 18, 2026
Python script to format metadata to table Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

nf-core/proteinfold#627 · Opened May 27, 2026
Add docs/development section for tips on contributors adding new modes Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/proteinfold#623 · Opened May 25, 2026
Create an --all_structs flag for populate_modelcif.py, capture *every* model & seed Open

nf-core/proteinfold#622 · 1 assignee · Opened May 25, 2026
Wire up a complete ASSEMBLE_MODECIF{} module to POST_PROCESSING{} for all modes Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/proteinfold#615 · Opened May 18, 2026
Extract tsv parsers from populated_modelcif.py into shared utils.py Open

duplicate

Difficulty 3/5 1-2 days Newbie friendliness 55/100

nf-core/proteinfold#614 · Opened May 18, 2026
Ensure all coordinates from the ensemble are stored in the modelCIF Open

nf-core/proteinfold#596 · 1 assignee · Opened May 4, 2026
Populate modelCIF atomic fields Open

nf-core/proteinfold#593 · 1 assignee · Opened Apr 30, 2026
Ensure the PAE as stored is openable in ChimeraX Open

nf-core/proteinfold#591 · 1 assignee · Opened Apr 23, 2026
Capture container image used to create structure Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

nf-core/proteinfold#590 · Opened Apr 21, 2026
Boltz multimer with precomputed MSAs with .yaml input Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

nf-core/proteinfold#589 · 1 comment · Opened Apr 20, 2026
populate_modelcif.py to handle the data ingest into classes Open

WIP

nf-core/proteinfold#584 · 1 assignee · Opened Apr 14, 2026
Compression of a metric-complete modelCIF? Open

question

nf-core/proteinfold#583 · 1 comment · 1 assignee · Opened Apr 14, 2026
Standardise metric file identities Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/proteinfold#581 · Opened Apr 14, 2026
Populate modelCIF software and protocol classes Open

enhancement

nf-core/proteinfold#579 · 3 comments · 1 assignee · Opened Apr 14, 2026
Populate modelCIF metrics classes Open

enhancement

nf-core/proteinfold#578 · 1 assignee · Opened Apr 14, 2026
PREPARE_COMMON_DBS() - simplify main.nf by ~30% Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 52/100

nf-core/proteinfold#575 · Opened Mar 31, 2026
Create micro db for boltz Open

WIP

nf-core/proteinfold#568 · 1 comment · 1 assignee · Opened Mar 18, 2026
Create wave container for EXTRACT_METRICS local module Open

enhancement

nf-core/proteinfold#562 · 4 comments · 1 assignee · Opened Mar 13, 2026
Split EXTRACT_METRICS for HelixFold3 Open

WIP

nf-core/proteinfold#548 · 1 assignee · Opened Mar 13, 2026
Split EXTRACT_METRICS for ESMFold Open

Ready for review

nf-core/proteinfold#547 · 1 assignee · Opened Mar 13, 2026
Split EXTRACT_METRICS for RoseTTAFold-All-Atom Open

Ready for review

nf-core/proteinfold#546 · 1 assignee · Opened Mar 13, 2026
Split EXTRACT_METRICS for ColabFold Open

Ready for review

nf-core/proteinfold#545 · 1 assignee · Opened Mar 13, 2026
Split EXTRACT_METRICS for RoseTTAFold2NA Open

help wanted

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/proteinfold#544 · Opened Mar 13, 2026
Split EXTRACT_METRICS for AlphaFold3 Open

help wanted

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/proteinfold#543 · Opened Mar 13, 2026
Split EXTRACT_METRICS for Boltz Open

Ready for review

nf-core/proteinfold#542 · 1 assignee · Opened Mar 13, 2026
Split EXTRACT_METRICS for AlphaFold2 Open

Ready for review

nf-core/proteinfold#541 · 1 assignee · Opened Mar 13, 2026
Create microDBs for AlphaFold3 Open

help wanted

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/proteinfold#534 · Opened Mar 12, 2026
Create microDBs for MMSEQS_COLABFOLDSEARCH Open

WIP

nf-core/proteinfold#533 · 1 assignee · Opened Mar 12, 2026
Update RUN_ALPHAFOLD2 for preparing the migration to modules Open

enhancement

nf-core/proteinfold#529 · 1 comment · 1 assignee · Opened Mar 11, 2026
Update RUN_BOLTZ for preparing the migration to modules Open

enhancement

nf-core/proteinfold#528 · 1 comment · 1 assignee · Opened Mar 11, 2026
Add SBF facility to report footer Open

documentation

nf-core/proteinfold#524 · 1 assignee · Opened Mar 11, 2026
MMseqs2 colabfoldsearch batching Open

enhancement

nf-core/proteinfold#521 · 1 assignee · Opened Mar 10, 2026
Add documentation for creating padded DBs Open

enhancement

nf-core/proteinfold#520 · 1 assignee · Opened Mar 10, 2026
Reduce size of mini dbs Open

WIP

nf-core/proteinfold#518 · 3 comments · 1 assignee · Opened Mar 10, 2026
Add DockQ v2 protein complex interface quality scoring Open

enhancement

nf-core/proteinfold#516 · 1 assignee · Opened Mar 9, 2026
Add US-align structural comparison and evaluation module Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/proteinfold#515 · Opened Mar 9, 2026
Mode-specific metromap Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/proteinfold#513 · Opened Mar 6, 2026
Additional clarity for reported metrics in TSV files. Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

nf-core/proteinfold#506 · Opened Mar 4, 2026
Add support for protenix v1 Open

enhancement

nf-core/proteinfold#505 · 1 assignee · Opened Mar 4, 2026
Improve MSA extraction from RoseTTAFold-All-Atom internal chain directories Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/proteinfold#491 · Opened Feb 20, 2026
Improve MSA processing robustness in Boltz module Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/proteinfold#490 · Opened Feb 20, 2026
Rename Boltz output channels to use format suffix (_npz, _tsv) Open

enhancement

nf-core/proteinfold#487 · 1 assignee · Opened Feb 20, 2026
Support cif files in boltz Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/proteinfold#486 · Opened Feb 20, 2026
Refactor generate_report.py: extract plotting utilities and clean up duplicated code Open

enhancement

nf-core/proteinfold#484 · 1 assignee · Opened Feb 20, 2026
Enable custom MSA input Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/proteinfold#479 · Opened Feb 16, 2026

nf-core/proteinfold

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