nf-core/proteinfold

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• Dependency clash in modules/local/fasta_to_alphafold3_json/environment.yml

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  bug

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

  nf-core/proteinfold#658 · Opened Oct 8, 2026

• config parsing failed

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

  nf-core/proteinfold#650 · 1 comment · Opened Aug 31, 2026

• BOLTZ_FASTA errors on more than 62 fasta entries

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  bug

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

  nf-core/proteinfold#637 · Opened Jun 26, 2026

• Downstream mmcif analysis

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  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

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  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

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  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

  May be free again @keiran-rowell-unsw claimed this 140 days ago, and no pull request is open. Open

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  nf-core/proteinfold#622 · 1 assignee · Opened May 25, 2026

• Wire up a complete ASSEMBLE_MODECIF{} module to POST_PROCESSING{} for all modes

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  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

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  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

  May be free again @keiran-rowell-unsw claimed this 150 days ago, and no pull request is open. Open

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  nf-core/proteinfold#596 · 1 assignee · Opened May 4, 2026

• Populate modelCIF atomic fields

  May be free again @keiran-rowell-unsw claimed this 150 days ago, and no pull request is open. Open

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  nf-core/proteinfold#593 · 1 assignee · Opened Apr 30, 2026

• Ensure the PAE as stored is openable in ChimeraX

  May be free again @keiran-rowell-unsw claimed this 147 days ago, and no pull request is open. Open

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  nf-core/proteinfold#591 · 1 assignee · Opened Apr 23, 2026

• Capture container image used to create structure

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  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

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

  nf-core/proteinfold#589 · 1 comment · Opened Apr 20, 2026

• Compression of a metric-complete modelCIF?

  May be free again @keiran-rowell-unsw claimed this 147 days ago, and no pull request is open. Open

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  question

  nf-core/proteinfold#583 · 1 comment · 1 assignee · Opened Apr 14, 2026

• Standardise metric file identities

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  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

  May be free again @keiran-rowell-unsw claimed this 145 days ago, and no pull request is open. Open

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  enhancement

  nf-core/proteinfold#579 · 3 comments · 1 assignee · Opened Apr 14, 2026

• Populate modelCIF metrics classes

  May be free again @keiran-rowell-unsw claimed this 165 days ago, and no pull request is open. Open

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  enhancement

  nf-core/proteinfold#578 · 1 assignee · Opened Apr 14, 2026

• Create micro db for boltz

  May be free again @jscgh claimed this 206 days ago, and no pull request is open. Open

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  WIP

  nf-core/proteinfold#568 · 1 comment · 1 assignee · Opened Mar 18, 2026

• Create wave container for EXTRACT_METRICS local module

  May be free again @JoseEspinosa claimed this 213 days ago, and no pull request is open. Open

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  enhancement

  nf-core/proteinfold#562 · 4 comments · 1 assignee · Opened Mar 13, 2026

• Split EXTRACT_METRICS for HelixFold3

  May be free again @jscgh claimed this 213 days ago, and no pull request is open. Open

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  WIP

  nf-core/proteinfold#548 · 1 assignee · Opened Mar 13, 2026

• Split EXTRACT_METRICS for ESMFold

  May be free again @jscgh claimed this 213 days ago, and no pull request is open. Open

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  Ready for review

  nf-core/proteinfold#547 · 1 assignee · Opened Mar 13, 2026

• Split EXTRACT_METRICS for RoseTTAFold-All-Atom

  May be free again @jscgh claimed this 213 days ago, and no pull request is open. Open

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  Ready for review

  nf-core/proteinfold#546 · 1 assignee · Opened Mar 13, 2026

• Split EXTRACT_METRICS for ColabFold

  May be free again @jscgh claimed this 213 days ago, and no pull request is open. Open

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  Ready for review

  nf-core/proteinfold#545 · 1 assignee · Opened Mar 13, 2026

• Split EXTRACT_METRICS for RoseTTAFold2NA

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  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

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  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

  May be free again @jscgh claimed this 213 days ago, and no pull request is open. Open

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  Ready for review

  nf-core/proteinfold#542 · 1 assignee · Opened Mar 13, 2026

• Split EXTRACT_METRICS for AlphaFold2

  May be free again @jscgh claimed this 213 days ago, and no pull request is open. Open

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  Ready for review

  nf-core/proteinfold#541 · 1 assignee · Opened Mar 13, 2026

• Create microDBs for AlphaFold3

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  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

  May be free again @jscgh claimed this 214 days ago, and no pull request is open. Open

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  WIP

  nf-core/proteinfold#533 · 1 assignee · Opened Mar 12, 2026

• Update RUN_ALPHAFOLD2 for preparing the migration to modules

  May be free again @alessiovignoli claimed this 215 days ago, and no pull request is open. Open

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  enhancement

  nf-core/proteinfold#529 · 1 comment · 1 assignee · Opened Mar 11, 2026

• Update RUN_BOLTZ for preparing the migration to modules

  May be free again @sblaizerwize claimed this 215 days ago, and no pull request is open. Open

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  enhancement

  nf-core/proteinfold#528 · 1 comment · 1 assignee · Opened Mar 11, 2026

• MMseqs2 colabfoldsearch batching

  May be free again @ziadbkh claimed this 215 days ago, and no pull request is open. Open

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  enhancement

  nf-core/proteinfold#521 · 1 assignee · Opened Mar 10, 2026

• Add documentation for creating padded DBs

  May be free again @nbtm-sh claimed this 215 days ago, and no pull request is open. Open

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  enhancement

  nf-core/proteinfold#520 · 1 assignee · Opened Mar 10, 2026

• Reduce size of mini dbs

  May be free again @jscgh claimed this 215 days ago, and no pull request is open. Open

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  WIP

  nf-core/proteinfold#518 · 3 comments · 1 assignee · Opened Mar 10, 2026

• Add DockQ v2 protein complex interface quality scoring

  May be free again @sudekaraoglan claimed this 213 days ago, and no pull request is open. Open

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  enhancement

  nf-core/proteinfold#516 · 1 assignee · Opened Mar 9, 2026

• Add US-align structural comparison and evaluation module

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  enhancement

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

  nf-core/proteinfold#515 · Opened Mar 9, 2026

• Mode-specific metromap

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  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.

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  enhancement

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

  nf-core/proteinfold#506 · Opened Mar 4, 2026

• Improve MSA extraction from RoseTTAFold-All-Atom internal chain directories

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  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

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  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)

  May be free again @keiran-rowell-unsw claimed this 195 days ago, and no pull request is open. Open

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  enhancement

  nf-core/proteinfold#487 · 1 assignee · Opened Feb 20, 2026

• Support cif files in boltz

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  enhancement

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

  nf-core/proteinfold#486 · Opened Feb 20, 2026

• Enable custom MSA input

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  enhancement

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

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

• Better support for running multiple replicates with different seeds.

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

  nf-core/proteinfold#478 · Opened Feb 16, 2026

• Support for sharded sequence database search

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  enhancement

  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  nf-core/proteinfold#477 · Opened Feb 16, 2026

• Split AlphaFold2 MSA search operations in to separate nextflow processes

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  enhancement

  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  nf-core/proteinfold#476 · Opened Feb 16, 2026

• multiqc/proteinfold for a 'bulk report'

  May be free again @keiran-rowell-unsw claimed this 279 days ago, and no pull request is open. Open

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  enhancement

  nf-core/proteinfold#439 · 5 comments · 1 assignee · Opened Jan 6, 2026

• Implement ci workflow to run bioflow-inside

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  enhancement

  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  nf-core/proteinfold#423 · Opened Dec 12, 2025

• Make it possible to render the metromap using the bioflow-inside online server

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  enhancement

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

  nf-core/proteinfold#422 · Opened Dec 12, 2025