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Testing out Reftrace for regex replacement in modules

Status: Draft (not ready).

nf-core/toolsnumber 3745

#3745 In nf-core/tools;

· ningyuxin1999 opened on Sep 2, 2025

create template GENERATE_DOWNSTREAM_SAMPLESHEETS for tools

Status: Draft (not ready).

nf-core/toolsnumber 3261

#3261 In nf-core/tools;

· Joon-Klaps opened on Oct 29, 2024

Add nf-core configs create sub command (attempt 2)

Status: Draft (not ready).

nf-core/toolsnumber 3001

#3001 In nf-core/tools;

· jfy133 opened on May 25, 2024

Add pipeline linting for configuration files such that all directives which use <code>params</code> are closures.

linting

Status: Open.

#2508 In nf-core/tools;

· mahesh-panchal opened on Nov 9, 2023

Migrate to nf-core-utils plugin

Status: Open.

Task

#3685 In nf-core/tools;

· edmundmiller opened on Jul 22, 2025

Fill out empty tests

house-keeping

linting

Status: Open.

#3728 In nf-core/tools;

· mashehu opened on Aug 27, 2025

TEMPLATE: add a fallback for new outputdir parameter

Status: Open (in progress).

nf-core/toolsnumber 3798

#3798 In nf-core/tools;

· mashehu opened on Oct 3, 2025

Leave old pipelines sync PRs open

Status: Open.

#3811 In nf-core/tools;

· mirpedrol opened on Oct 7, 2025

'modules lint' and 'subworkflow lint' should also ignore files from .gitignore

linting

Status: Open.

#3529 In nf-core/tools;

· Gullumluvl opened on Apr 3, 2025

Subworkflow install failure still results in a 0 exit code

bugSomething isn't workingSomething isn't working

Status: Open.

#3044 In nf-core/tools;

· jvfe opened on Jul 1, 2024

Add link to release blog post on sync PRs

Status: Open.

#3812 In nf-core/tools;

· mirpedrol opened on Oct 7, 2025

Update AWS Mega Test CI workflow to use new variables for GPU and ARM Megatests

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

Status: Open.

Enhancement

#3692 In nf-core/tools;

· edmundmiller opened on Jul 29, 2025

Use outputDir in nf-core pipelines

Status: Open.

Enhancement

#3707 In nf-core/tools;

· edmundmiller opened on Aug 8, 2025

Remove nf-test latest for PRs and run nf-test latest on PR merge

Status: Open.

Enhancement

#3768 In nf-core/tools;

· edmundmiller opened on Sep 23, 2025

Download pipelines with authenticated GH API calls

Status: Open (in progress).

nf-core/toolsnumber 3607

#3607 In nf-core/tools;

· jpfeuffer opened on Jun 5, 2025

Lint for version captures in modules

Status: Open (in progress).

nf-core/toolsnumber 3676

#3676 In nf-core/tools;

· edmundmiller opened on Jul 11, 2025

General: add pytest for get_wf_files

Status: Open (in progress).

nf-core/toolsnumber 3725

#3725 In nf-core/tools;

· mirpedrol opened on Aug 26, 2025

Change devcontainer to install tools at current commit

enhancement

Status: Open.

#3837 In nf-core/tools;

· JulianFlesch opened on Oct 15, 2025

nf-core linting parsing emit output as path

bugSomething isn't workingSomething isn't working

linting

Status: Open.

Bug

#3842 In nf-core/tools;

· dialvarezs opened on Oct 21, 2025

Wrong min. python version in bioconda recipe

bugSomething isn't workingSomething isn't working

Status: Open.

#3843 In nf-core/tools;

· FriederikeHanssen opened on Oct 21, 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

sync: Keep automated template update PRs open

Status: Open (in progress).

nf-core/toolsnumber 3851

#3851 In nf-core/tools;

· mashehu opened on Oct 28, 2025