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--empty-template flag not producing fully empty module template

bugSomething isn't workingSomething isn't working

Status: Open.

#4054 In nf-core/tools;

· vagkaratzas opened on Feb 20, 2026

<code>nf-core subworkflows lint &lt;name&gt; --local</code> does not work for subworkflows in <code>subworkflows/local</code>

bugSomething isn't workingSomething isn't working

Status: Open.

#4049 In nf-core/tools;

· nschan opened on Feb 18, 2026

Container Linting for Modules

Status: Open.

#4041 In nf-core/tools;

· JulianFlesch opened on Feb 12, 2026

nf-core update all depencencies (modules + subworkflows)

enhancement

Status: Open.

#4031 In nf-core/tools;

· maxulysse opened on Feb 6, 2026

<code>nf-core pipeline downloads</code> issues when downloading pipelines for <code>--platform</code>

bugSomething isn't workingSomething isn't working

downloadnf-core downloadnf-core download

Status: Open.

#4028 In nf-core/tools;

· MatthiasZepper opened on Feb 4, 2026

Idea: Roll out 'PR labeler' GitHub action to all pipeline (and modules) via template

enhancement

Status: Open.

#4025 In nf-core/tools;

· jfy133 opened on Feb 2, 2026

Re-test and label/exclude modules with failing tests

Status: Open.

#4016 In nf-core/tools;

· pinin4fjords opened on Jan 30, 2026

type dir output

Status: Open.

#3989 In nf-core/tools;

· maxulysse opened on Jan 20, 2026

Support version topic channels with val rather than eval for versions

enhancement

Status: Open.

#3985 In nf-core/tools;

· prototaxites opened on Jan 16, 2026

Linting a module with "hidden: true" carries this part of the text into the meta.yml

bugSomething isn't workingSomething isn't working

Status: Open.

#3983 In nf-core/tools;

· prototaxites opened on Jan 16, 2026

Define the correct schema when creating a cross-org sub-workflow

enhancement

Status: Open.

#3981 In nf-core/tools;

· muffato opened on Jan 13, 2026

no test_full profile fails the download CI

enhancement

Status: Open.

#3979 In nf-core/tools;

· maxulysse opened on Jan 8, 2026