1 Release published by 1 person

• 3.3.2 v3.3.2 - Tungsten Tamarin Patch 2

  published Jul 8, 2025

11 Pull requests merged by 4 people

• bump version to 3.4.0dev

  #3670 merged Jul 9, 2025

• fix version number

  #3669 merged Jul 8, 2025

• Dev -> main for 3.3.2

  #3664 merged Jul 8, 2025

• bump version to 3.3.2

  #3666 merged Jul 8, 2025

• downgrade to nf-version 24.10.5

  #3667 merged Jul 8, 2025

• Fix wrong key when updating module outputs

  #3665 merged Jul 8, 2025

• Update python:3.13-slim Docker digest to 6544e0e

  #3663 merged Jul 8, 2025

• Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.2

  #3661 merged Jul 8, 2025

• Enable parsing of multi-line config values

  #3629 merged Jul 7, 2025

• Update nf-core modules info command after meta.yml restructuring

  #3659 merged Jul 7, 2025

• Fix modules meta.yml file structure

  #3532 merged Jul 7, 2025

6 Pull requests opened by 5 people

• Add autocompletion for modules / subworkflows and pipeline

  #3660 opened Jul 8, 2025

• Update dependency textual to v3.7.0

  #3662 opened Jul 8, 2025

• Update nf-test.yml

  #3673 opened Jul 9, 2025

• don't read param expressions with spaces as params

  #3674 opened Jul 10, 2025

• template - adding new multiqc file llms-full.txt to nftignore file

  #3675 opened Jul 10, 2025

• Lint for version captures in modules

  #3676 opened Jul 11, 2025

2 Issues closed by 2 people

• Inconsistent number of containers with `pipelines download` subcommand

  #3551 closed Jul 13, 2025

• Modules meta.yml differentiate between tuple and single element channels

  #3248 closed Jul 7, 2025

3 Issues opened by 3 people

• schema_params linting is failing when a = is in the args

  #3672 opened Jul 9, 2025

• Handle pipelines without `manifest.contributors` in the `nextrflow.config` during pipeline sync

  #3671 opened Jul 9, 2025

• Modules yaml schemes don't follow nf-core releases

  #3668 opened Jul 7, 2025

18 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• WIP: Refactor pipeline downloads command

  #3634 commented on Jul 11, 2025 • 40 new comments

• Fix #3655: Allow dots (.), hyphens (-), and underscores (_) in GitHub usernames

  #3658 commented on Jul 12, 2025 • 4 new comments

• feat: nf-core modules bump-version supports specifying the toolkit

  #3608 commented on Jul 7, 2025 • 4 new comments

• Issues/3466 Move away from Gitpod

  #3569 commented on Jul 8, 2025 • 1 new comment

• Refactor module lint tests

  #3592 commented on Jul 8, 2025 • 0 new comments

• Update conda env sorting

  #3591 commented on Jul 11, 2025 • 0 new comments

• create template GENERATE_DOWNSTREAM_SAMPLESHEETS for tools

  #3261 commented on Jul 8, 2025 • 0 new comments

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

  #3001 commented on Jul 8, 2025 • 0 new comments

• Renovate Dashboard 🤖

  #2596 commented on Jul 12, 2025 • 0 new comments

• `pipelines download` not working as expected?

  #3490 commented on Jul 10, 2025 • 0 new comments

• Subworkflow install failure still results in a 0 exit code

  #3044 commented on Jul 8, 2025 • 0 new comments

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

  #3529 commented on Jul 8, 2025 • 0 new comments

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

  #2492 commented on Jul 8, 2025 • 0 new comments

• Add pipeline linting for configuration files such that all directives which use `params` are closures.

  #2508 commented on Jul 8, 2025 • 0 new comments

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

  #3140 commented on Jul 8, 2025 • 0 new comments

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

  #3174 commented on Jul 8, 2025 • 0 new comments

• Deprecate gitpod, update devcontainer.json for GitHub codespaces

  #3466 commented on Jul 8, 2025 • 0 new comments

• Check for import in all workflows

  #3479 commented on Jul 8, 2025 • 0 new comments