nf-core/funcscan

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(Meta-)genome screening for functional and natural product gene sequences

Stars: 119
Forks: 40
Open beginner issues: 0
Indexed issues: 19
Avg merge: 2d 17h
Merged PRs (30d): 5

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 24, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

Open All

19 open issues indexed

MultiQC report not displaying all all samples for bakta/prokka Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 55/100

nf-core/funcscan#544 · Opened Aug 28, 2026
prodigal process expects gzipped file Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 42/100

nf-core/funcscan#541 · Opened Jul 28, 2026
ARG gene symbols are not standardized across tools in hAMRonization summary, making cross-tool comparison difficult Open

enhancement

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

nf-core/funcscan#525 · 4 comments · Opened Apr 16, 2026
AMPCOMBI2_PARSETABLES error during stage-out with process.stageOutMode = 'move' -- "mv: cannot stat 'XYZ': No such file or directory" Open

bug

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

nf-core/funcscan#524 · Opened Apr 5, 2026
Add BiG-SCAPE Open

enhancement

nf-core/funcscan#509 · 2 comments · 1 reaction · 1 assignee · Opened Dec 9, 2025
Bug in ARG + taxonomy merging Open

bug requires-upstream-fix

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

nf-core/funcscan#491 · 3 comments · Opened Aug 14, 2025
Fix eventual ampcombi_parsetables crash Open

enhancement requires-upstream-fix

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

nf-core/funcscan#489 · Opened Jul 22, 2025
Update argNorm to current version Open

enhancement

nf-core/funcscan#487 · 1 comment · 1 assignee · Opened Jul 17, 2025
Add support for reading external InterProScan results as pipeline input Open

enhancement

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

nf-core/funcscan#485 · Opened Jul 9, 2025
Integrate the existing eggNOG-mapper module into the pipeline Open

enhancement

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

nf-core/funcscan#473 · 1 reaction · Opened Apr 13, 2025
Add support for generating mmseqs taxonomy reports Open

enhancement

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

nf-core/funcscan#466 · 2 comments · 2 reactions · Opened Mar 21, 2025
How to speed up MMseqs2 taxonomy assignment with GTDB database on large contigs? Open

question

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

nf-core/funcscan#424 · 1 comment · Opened Oct 18, 2024
A uniform input for all tools in each screening workflow Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

nf-core/funcscan#385 · 2 comments · Opened Jun 5, 2024
Add module: resfinder Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 42/100

nf-core/funcscan#330 · Opened Jan 23, 2024
Adapt deepBGC to use GPUs Open

enhancement

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

nf-core/funcscan#326 · 4 comments · Opened Dec 19, 2023
Add pharokka to nf-core/funcscan Open

feature-request

nf-core/funcscan#329 · 1 assignee · Opened Dec 15, 2023
Benchmarking tests showing resource values are suboptimal Open

bug low-priority

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

nf-core/funcscan#292 · Opened Jul 5, 2023
Consider adding annotation tools to MultiQC report Open

enhancement

nf-core/funcscan#277 · 1 assignee · Opened May 24, 2023
Consider passing the annotation tool output to modules input for more standardization Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/funcscan#179 · Opened Dec 21, 2022

nf-core/funcscan

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