List view

Expand fasta_to_alphafold3_json.py to support multifasta multimers

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

Bug

#325 In nf-core/proteinfold;

· keiran-rowell-unsw opened on Jun 10, 2025

Add Chai-1

feature-requestRequest for a new pipeline featureRequest for a new pipeline feature

Status: Open.

Enhancement

#250 In nf-core/proteinfold;

· jscgh opened on Feb 28, 2025

Update colabfold_batch subworkflow

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#224 In nf-core/proteinfold;

· luisas opened on Nov 21, 2024

Add checksums validation for DBs files

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#107 In nf-core/proteinfold;

· JoseEspinosa opened on Jun 15, 2023

colabfold_local mode does not work offline

bugSomething isn't workingSomething isn't working

Status: Open.

#209 In nf-core/proteinfold;

· JoseEspinosa opened on Oct 29, 2024

Add download of Foldseek DBs

enhancementImprovement for existing functionalityImprovement for existing functionality

feature-requestRequest for a new pipeline featureRequest for a new pipeline feature

Status: Open.

Enhancement

#288 In nf-core/proteinfold;

· JoseEspinosa opened on Apr 9, 2025

Adding interaction screening feature

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#258 In nf-core/proteinfold;

· ziadbkh opened on Mar 24, 2025

Create a process for extract_metrics.py

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

Enhancement

#309 In nf-core/proteinfold;

· JoseEspinosa opened on May 19, 2025

Support *.cif.gz or *.gz files detection for all DBs in AF2 pipeline

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#279 In nf-core/proteinfold;

· MauriAndresMU1313 opened on Mar 27, 2025

Should the downloading subworkflow become a separate workflow?

enhancementImprovement for existing functionalityImprovement for existing functionality

questionFurther information is requestedFurther information is requested

Status: Open.

#203 In nf-core/proteinfold;

· JoseEspinosa opened on Oct 25, 2024

nextflow_schema.json is not working on seqera platform

bugSomething isn't workingSomething isn't working

Status: Open.

#206 In nf-core/proteinfold;

· ziadbkh opened on Oct 26, 2024

Integrate Jalview for the visualisation of AlphaFold2 and Colabfold results

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#86 In nf-core/proteinfold;

· athbaltzis opened on Mar 26, 2023

Improved support for non-protein entities

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#353 In nf-core/proteinfold;

· tlitfin-unsw opened on Aug 3, 2025

nf-tests do not capture versions from container contents

bugSomething isn't workingSomething isn't working

Status: Open.

Bug

#365 In nf-core/proteinfold;

· jscgh opened on Aug 6, 2025

Change to named instead of positional arguments in channel mixing

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

Bug

#373 In nf-core/proteinfold;

· keiran-rowell-unsw opened on Aug 13, 2025

MSA coverage plot in HTML report, for every module

bugSomething isn't workingSomething isn't working

Status: Open.

Bug

#363 In nf-core/proteinfold;

· keiran-rowell-unsw opened on Aug 6, 2025

Minimal value dummy tsv for each metric until GENERATE_REPORT is refactored

bugSomething isn't workingSomething isn't working

Status: Open.

Enhancement

#375 In nf-core/proteinfold;

· keiran-rowell-unsw opened on Aug 20, 2025

Switch from stub run tests to use small DBs

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#400 In nf-core/proteinfold;

· JoseEspinosa opened on Oct 14, 2025

Toggle color between confidence and chain in HTML report.

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#411 In nf-core/proteinfold;

· tlitfin opened on Nov 18, 2025

Implement automatic metro map generation using bioflow-insight-metro-map tool

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#421 In nf-core/proteinfold;

· JoseEspinosa opened on Dec 12, 2025

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

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#422 In nf-core/proteinfold;

· JoseEspinosa opened on Dec 12, 2025

Implement ci workflow to run bioflow-inside

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#423 In nf-core/proteinfold;

· JoseEspinosa opened on Dec 12, 2025

multiqc/proteinfold for a 'bulk report'

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

Enhancement

#439 In nf-core/proteinfold;

· keiran-rowell-unsw opened on Jan 6, 2026

Refactor local modules

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#183 In nf-core/proteinfold;

· JoseEspinosa opened on Oct 2, 2024

Current index of _plddt.tsv file can lead to mis-matched outputs.

bugSomething isn't workingSomething isn't working

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#456 In nf-core/proteinfold;

· tlitfin opened on Jan 30, 2026