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Implement wave container commands

Status: Open (in progress).

nf-core/toolsnumber 3954

#3954 In nf-core/tools;

· JulianFlesch opened on Dec 2, 2025

Request org details to fill in more template fields

Status: Draft (not ready).

nf-core/toolsnumber 4146

#4146 In nf-core/tools;

· muffato opened on Mar 29, 2026

Migrate to nf-core-utils plugin

high-priority

templatenf-core pipeline/component templatenf-core pipeline/component template

Status: Open.

Task

#3685 In nf-core/tools;

· edmundmiller opened on Jul 22, 2025

nf-core modules lint fails on patched modules with modified inputs/outputs

bugSomething isn't workingSomething isn't working

Status: Open.

#3772 In nf-core/tools;

· svarona opened on Sep 25, 2025

Linting a subworkflow meta YML with components not present in the workflow throws a linting error

bugSomething isn't workingSomething isn't working

linting

Status: Open.

#3844 In nf-core/tools;

· prototaxites opened on Oct 21, 2025

nf-core modules lint --fix produces mangled output

bugSomething isn't workingSomething isn't working

Status: Open.

#3901 In nf-core/tools;

· TCLamnidis opened on Nov 14, 2025

Pipeline template: New pre-commit hooks (large files, merge conflicts)

Status: Open (in progress).

nf-core/toolsnumber 3935

#3935 In nf-core/tools;

· MatthiasZepper opened on Nov 26, 2025

Handle deprecated and deleted modules/subworkflows gracefully

enhancement

Status: Open.

#4260 In nf-core/tools;

· SPPearce opened on May 5, 2026

meta.json stub file trips up meta_nf_meta_key linting

bugSomething isn't workingSomething isn't working

Status: Open.

#4250 In nf-core/tools;

· DLBPointon opened on Apr 29, 2026