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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

Refactor module lint tests

awaiting-feedback

Status: Draft (not ready).

nf-core/toolsnumber 3592

#3592 In nf-core/tools;

· edmundmiller opened on May 30, 2025

Update conda env sorting

awaiting-changesNeeds changes after a review. Remove label when ready to be reviewed again.Needs changes after a review. Remove label when ready to be reviewed again.

Status: Open (in progress).

nf-core/toolsnumber 3591

#3591 In nf-core/tools;

· edmundmiller opened on May 30, 2025

Issues/3466 Move away from Gitpod

Status: Draft (not ready).

nf-core/toolsnumber 3569

#3569 In nf-core/tools;

· JulianFlesch opened on May 14, 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

Check for import in all workflows

bugSomething isn't workingSomething isn't working

Status: Open.

#3479 In nf-core/tools;

· LouisLeNezet opened on Mar 5, 2025

Deprecate gitpod, update devcontainer.json for GitHub codespaces

good-first-issue

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

Status: Open.

#3466 In nf-core/tools;

· kenibrewer opened on Feb 24, 2025

Add ability to install a nf-core module into a private module library

enhancement

high-priority

Status: Open.

#3174 In nf-core/tools;

· kenibrewer opened on Sep 17, 2024

Pass a list of modules/subworkflows(files) to nf-core modules lint

enhancement

high-priority

Status: Open.

#3140 In nf-core/tools;

· edmundmiller opened on Aug 26, 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

Add --no-tests flag to nf-core modules install

nf-test

pipeline-testing

Status: Open.

#2492 In nf-core/tools;

· edmundmiller opened on Oct 24, 2023

'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