nf-core/modules

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Repository to host tool-specific module files for the Nextflow DSL2 community!

Stars: 429
Forks: 1.1k
Open beginner issues: 0
Indexed issues: 314
Avg merge: 1d 6h
Merged PRs (30d): 153

Dominant language: Nextflow
License: MIT
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue help wanted

Beginner friendly Everything

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314 open issues indexed

[FEATURE] polyglot runtime and publishable Distroless image Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

nf-core/modules#12997 · Opened Sep 19, 2026
update module: SHOVILL Open

update module

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

nf-core/modules#12980 · Opened Sep 16, 2026
new module: metaproviz/internalstandard Open

new module

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

nf-core/modules#12957 · 1 comment · Opened Sep 15, 2026
new module: PSAURON Open

new module

nf-core/modules#12956 · 1 assignee · Opened Sep 14, 2026
Migrate to topic: universc Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/modules#12951 · Opened Sep 14, 2026
Migrate to topic: narfmap/hashtable Open

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

nf-core/modules#12944 · Opened Sep 14, 2026
Migrate to topic: multiqc Open

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

nf-core/modules#12943 · 1 comment · Opened Sep 14, 2026
Migrate to topic: multiqcsav Open

Difficulty 4/5 3-5 days Newbie friendliness 15/100

nf-core/modules#12942 · 1 comment · Opened Sep 14, 2026
New module: motifmatchr/matchmotifs Open

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

nf-core/modules#12926 · Opened Sep 10, 2026
New module: tobias/bindetect Open

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

nf-core/modules#12924 · Opened Sep 10, 2026
new module: telomerehunter2 Open

new module wishlist

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

nf-core/modules#12916 · Opened Sep 10, 2026
New module: nucleoatac Open

new module wishlist

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

nf-core/modules#12914 · Opened Sep 10, 2026
Adopt topic channels in all nf-core modules [PART 8] Open

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

nf-core/modules#12884 · Opened Sep 3, 2026
`manta/germline`: pinned container segfaults in `GenerateSVCandidates` on WGS trios Open

bug

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

nf-core/modules#12881 · Opened Sep 3, 2026
New modules: STAR Suite alignment and genome generation Open

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

nf-core/modules#12825 · Opened Aug 27, 2026
new module: HYPHY/RELAX Open

new module

nf-core/modules#12810 · 1 assignee · Opened Aug 26, 2026
new module: HYPHY/various tools Open

new module

nf-core/modules#12802 · 1 assignee · Opened Aug 26, 2026
Topics migration: Problematic modules Open

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

nf-core/modules#12792 · 1 comment · Opened Aug 25, 2026
hmmer/hmmrank: multi-model domtblout multiplies rank rows and unions coordinates across profiles Open

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

nf-core/modules#12787 · Opened Aug 25, 2026
Migrate to topic starfusion/build Open

nf-core/modules#12734 · 1 assignee · Opened Aug 18, 2026
new module: cnvkit/referencepooled Open

new module wishlist

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

nf-core/modules#12668 · Opened Aug 13, 2026
update module: cellranger Open

update module

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

nf-core/modules#12660 · 1 comment · Opened Aug 12, 2026
[FEATURE] Support generating a pooled reference in cnvkit/reference Open

Difficulty 3/5 1-2 days Newbie friendliness 64/100

nf-core/modules#12656 · 2 comments · Opened Aug 11, 2026
Port aspera_cli from fetchngs to the modules repo Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/modules#12649 · Opened Aug 11, 2026
bakta/bakta: gzip output files Open

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

nf-core/modules#12643 · Opened Aug 10, 2026
new module: STRAGLR Open

new module

nf-core/modules#12640 · 1 assignee · Opened Aug 9, 2026
new module: isocall/assignreads Open

new module

nf-core/modules#12595 · 1 assignee · Opened Aug 5, 2026
new module: isocall/call Open

new module

nf-core/modules#12594 · 1 assignee · Opened Aug 5, 2026
new module: isocall/merge Open

new module

nf-core/modules#12593 · 1 assignee · Opened Aug 5, 2026
new module: isocall/profile Open

new module

nf-core/modules#12592 · 1 assignee · Opened Aug 5, 2026
new module: isocall/prepisoforms Open

new module

nf-core/modules#12591 · 1 assignee · Opened Aug 5, 2026
Sentieon License file resolution breaks if not supplied Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/modules#12544 · Opened Aug 4, 2026
Migrate to topic repeatmodeler/repeatmodeler Open

nf-core/modules#12511 · 1 assignee · Opened Aug 3, 2026
Migrate to topic repeatmodeler/builddatabase Open

nf-core/modules#12510 · 1 assignee · Opened Aug 3, 2026
Adopt topic channels in all nf-core modules [PART 7] Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/modules#12502 · Opened Aug 3, 2026
fmh-funprofiler silent errors Open

bug

nf-core/modules#12416 · 1 assignee · Opened Jul 23, 2026
update module: FASTP Open

update module

nf-core/modules#12397 · 1 comment · 1 assignee · Opened Jul 22, 2026
update module: BCFTOOLS/MERGE Open

update module

nf-core/modules#12373 · 1 assignee · Opened Jul 15, 2026
Migrate to topic narfmap/hashtable Open

nf-core/modules#12319 · 1 comment · 1 assignee · Opened Jul 8, 2026
new module: presto/assemblepairs Open

new module wishlist

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

nf-core/modules#12225 · Opened Jul 1, 2026
new module: ciri2 Open

new module wishlist

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/modules#12223 · 2 comments · Opened Jul 1, 2026
new module: presto/pairseq Open

new module wishlist

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

nf-core/modules#12206 · Opened Jun 30, 2026
new module: EUBIBRIDGE Open

new module

nf-core/modules#12204 · 1 assignee · Opened Jun 30, 2026
new module: primer3 Open

new module

nf-core/modules#12199 · 1 assignee · Opened Jun 30, 2026
update module: presto/filterseq Open

update module

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

nf-core/modules#12192 · Opened Jun 29, 2026
gatk4/postprocessgermlinecnvcalls incorrect file type extension Open

bug

nf-core/modules#12169 · 1 comment · 1 assignee · Opened Jun 25, 2026
new module: griffin/gc_correct Open

new module

nf-core/modules#12120 · 1 assignee · Opened Jun 22, 2026
new module: refinegems Open

new module

nf-core/modules#11934 · 1 reaction · 2 assignees · Opened Jun 9, 2026
Migrate to topic lissero Open

nf-core/modules#11908 · 1 assignee · Opened Jun 8, 2026
Adopt topic channels in all nf-core modules [PART 6] Open

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

nf-core/modules#11898 · Opened Jun 8, 2026

nf-core/modules

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