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Add AST-grep lint foundations

Status: Open (in progress).

nf-core/toolsnumber 4377

#4377 In nf-core/tools;

· edmundmiller opened on Jul 7, 2026

Flag legacy versions.yml topic outputs

Status: Open (in progress).

nf-core/toolsnumber 4379

#4379 In nf-core/tools;

· edmundmiller opened on Jul 7, 2026

Flag legacy versions emits

Status: Open (in progress).

nf-core/toolsnumber 4380

#4380 In nf-core/tools;

· edmundmiller opened on Jul 7, 2026

Migrate pipeline lint rules to AST-grep

Status: Open (in progress).

nf-core/toolsnumber 4381

#4381 In nf-core/tools;

· edmundmiller opened on Jul 7, 2026

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

Linting or GHA to test whether all modules of a module suite are updated

enhancement

linting

modulesRelated to tools for working with DSL2 modulesRelated to tools for working with DSL2 modules

Status: Open.

#4355 In nf-core/tools;

· famosab opened on Jun 26, 2026

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

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

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

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