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update module: PERBASE

update module

Status: Open.

#9794 In nf-core/modules;

· camlloyd opened on Jan 28, 2026

Bump BCFTOOLS version to 1.23

update module

Status: Open.

#9792 In nf-core/modules;

· georgiakes opened on Jan 28, 2026

new module: CELLPOSE-SAM

new moduleAdding a new moduleAdding a new module

Status: Open.

#9791 In nf-core/modules;

· sebgoti opened on Jan 28, 2026

new subworkflow: fasta/consensus/autocycler

new subworkflow

Status: Open.

#9785 In nf-core/modules;

· dwells-eit opened on Jan 27, 2026

gatk4 - convert versions from modules to topics

Status: Open.

#9738 In nf-core/modules;

· maxulysse opened on Jan 22, 2026

new module: intervene/upset

new moduleAdding a new moduleAdding a new module

Status: Open.

#9706 In nf-core/modules;

· asntech opened on Jan 20, 2026

new module: stainwarpy/transformsegmask

imaging

new moduleAdding a new moduleAdding a new module

wishlistclosed after a year if no one assignedclosed after a year if no one assigned

Status: Open.

#9703 In nf-core/modules;

· tckumarasekara opened on Jan 20, 2026

new module: stainwarpy/register

imaging

new moduleAdding a new moduleAdding a new module

wishlistclosed after a year if no one assignedclosed after a year if no one assigned

Status: Open.

#9702 In nf-core/modules;

· tckumarasekara opened on Jan 20, 2026

new modules: stainwarpy/extractchannel

imaging

new moduleAdding a new moduleAdding a new module

wishlistclosed after a year if no one assignedclosed after a year if no one assigned

Status: Open.

#9701 In nf-core/modules;

· tckumarasekara opened on Jan 20, 2026

new module: ViralConsensus

new moduleAdding a new moduleAdding a new module

wishlistclosed after a year if no one assignedclosed after a year if no one assigned

Status: Open.

#9653 In nf-core/modules;

· lucaspatel opened on Jan 14, 2026

Multiple uses of seqkit replace module fail due to output/input name conflicts

bugSomething isn't workingSomething isn't working

Status: Open.

#9647 In nf-core/modules;

· ammaraziz opened on Jan 14, 2026

seqkit replace incorrectly uses the '-i' flag

bugSomething isn't workingSomething isn't working

Status: Open.

#9646 In nf-core/modules;

· ammaraziz opened on Jan 14, 2026