Merge branch 'dev' into update/mqc1.31

Author: mirpedrol

.github/RELEASE_CHECKLIST.md

@@ -7,17 +7,19 @@
 5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:latest`.
 6. Make sure all CI tests are passing!
 7. Create a PR from `dev` to `main`
-8. Make sure all CI tests are passing again (additional tests are run on PRs to `main`)
-9. Request review (2 approvals required)
-10. Merge the PR into `main`
-11. Wait for CI tests on the commit to passed
-12. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
-13. Create a new release copying the `CHANGELOG` for that release into the description section.
+8. Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR: use the `Sync template` GitHub Action from the tools repository specifying the pipeline name and running from the `dev` branch.
+9. Warn someone from Seqera to make sure that the Seqera Platform is working as expected with the new template: use the `nf-core/testpipeline` new branch with the template updates.
+10. Make sure all CI tests are passing again (additional tests are run on PRs to `main`)
+11. Request review (2 approvals required)
+12. Merge the PR into `main`
+13. Wait for CI tests on the commit to passed
+14. Create a new release copying the `CHANGELOG` for that release into the description section.
 
 ## After release
 
-1. Check the automated template synchronisation has been triggered properly. This should automatically open PRs directly to individual pipeline repos with the appropriate changes to update the pipeline template.
-2. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
-3. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065)
-4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:dev`.
-5. Run `rich-codex` on the [tools/website repo](https://github.com/nf-core/website/actions/workflows/rich-codex.yml) to regenerate docs screengrabs (actions `workflow_dispatch` button)
+1. Run the `Sync template` GitHub Action to trigger the template update PR to some selected pipelines (sarek, createtaxdb, proteinfold, mag, #team-maintainers channel) and ask the pipeline maintainers to make the update and report any issues/comments.
+2. Run `rich-codex` to regenerate docs screengrabs: `Generate images for docs` GitHub Action on the [tools/website repo](https://github.com/nf-core/website/actions/workflows/rich-codex.yml).
+3. Manually trigger the `Sync template` GitHub Action for all pipelines.
+4. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
+5. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065)
+6. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:dev`.

.github/workflows/push_dockerhub_dev.yml

@@ -31,7 +31,7 @@ jobs:
         uses: docker/setup-buildx-action@e468171a9de216ec08956ac3ada2f0791b6bd435 # v3
 
       - name: Log in to Docker Hub
-        uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772 # v3
+        uses: docker/login-action@5e57cd118135c172c3672efd75eb46360885c0ef # v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASS }}

.github/workflows/push_dockerhub_release.yml

@@ -31,7 +31,7 @@ jobs:
         uses: docker/setup-buildx-action@e468171a9de216ec08956ac3ada2f0791b6bd435 # v3
 
       - name: Log in to Docker Hub
-        uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772 # v3
+        uses: docker/login-action@5e57cd118135c172c3672efd75eb46360885c0ef # v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASS }}

.github/workflows/pytest.yml

@@ -179,7 +179,7 @@ jobs:
           coverage report
           coverage xml
 
-      - uses: codecov/codecov-action@18283e04ce6e62d37312384ff67231eb8fd56d24 # v5
+      - uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5
         with:
           files: coverage.xml
           disable_search: true # we already know the file to upload

.github/workflows/test_offline_configs.yml

@@ -98,7 +98,7 @@ jobs:
 
       - name: Create Issue on Test Failure
         if: ${{ failure() }}
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
+        uses: actions/github-script@f28e40c7f34bde8b3046d885e986cb6290c5673b # v7
         with:
           github-token: ${{ secrets.nf_core_bot_auth_token }}
           script: |

.github/workflows/tools-api-docs.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: trigger API docs build
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
+        uses: actions/github-script@f28e40c7f34bde8b3046d885e986cb6290c5673b # v7
         with:
           github-token: ${{ secrets.nf_core_bot_auth_token }}
           script: |

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.7
+    rev: v0.13.3
     hooks:
       - id: ruff-check # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -12,7 +12,7 @@ repos:
         additional_dependencies:
           - [email protected]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
@@ -32,7 +32,7 @@ repos:
               tests/pipelines/__snapshots__/.*
           )$
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.17.1"
+    rev: "v1.18.2"
     hooks:
       - id: mypy
         additional_dependencies:

CHANGELOG.md

@@ -5,24 +5,29 @@
 ### Template
 
 - Update the `download_pipeline` workflow to remove dependency on `dev` branch of tools ([#3734](https://github.com/nf-core/tools/pull/3734))
+- Update mastodon announcement to include pipeline description ([#3741](https://github.com/nf-core/tools/pull/3741))
 - Bump nf-schema to 2.5.0 and update the help message creation to be compatible with future Nextflow versions ([#3743](https://github.com/nf-core/tools/pull/3743))
 - Bump minimum Nextflow version to 25.04.0 ([#3743](https://github.com/nf-core/tools/pull/3743))
 - Explicitly declare conda-forge as a channel in the conda setup for GitHub CI for nf-test ([#3764](https://github.com/nf-core/tools/pull/3764))
 - Update multiqc to 1.31 ([#3766](https://github.com/nf-core/tools/pull/3766))
 - Update charliecloud URL ([#3757](https://github.com/nf-core/tools/pull/3757))
 - Fix: Add NXF_VERSION environment variable to nf-test workflow ([#3770](https://github.com/nf-core/tools/pull/3770))
+- Template: Update nextflow.config to use environment variable for `hook_url` ([#3756](https://github.com/nf-core/tools/pull/3756))
 - Update nf-test to 0.9.3 ([#3781](https://github.com/nf-core/tools/pull/3781))
+- update release checklist to battle test pipeline template more ([#3788](https://github.com/nf-core/tools/pull/3788))
 
 ### Linting
 
 - ignore files in gitignore also for pipeline_if_empty_null lint test ([#3722](https://github.com/nf-core/tools/pull/3722))
 - do not check pytest_modules.yml file, deprecating ([#3748](https://github.com/nf-core/tools/pull/3748))
 - Use the org from the .nf-core.yml when linting manifest name and homePage. ([#3767](https://github.com/nf-core/tools/pull/3767))
+- Use the org from .nf-core.yml when linting multiqc_config report_comment ([#3800](https://github.com/nf-core/tools/pull/3800))
 
 ### Modules
 
 - Support modules with `exec:` blocks ([#3633](https://github.com/nf-core/tools/pull/3633))
 - feat: nf-core modules bump-version supports specifying the toolkit ([#3608](https://github.com/nf-core/tools/pull/3608))
+- Override example keywords in modules test ([#3801](https://github.com/nf-core/tools/pull/3801))
 
 ### Subworkflows
 
@@ -47,13 +52,25 @@
 - Move `gather_registries` function to `ContainerFetcher` subclasses (#3634 follow-up) ([#3696](https://github.com/nf-core/tools/pull/3696))
 - Add container load scripts for Docker and Podman (#3634 follow up) ([#3706](https://github.com/nf-core/tools/pull/3706))
 - Replace arm profile with arm64 and emulate_amd64 profiles ([#3689](https://github.com/nf-core/tools/pull/3689))
+- Update codecov/codecov-action digest to fdcc847 ([#3717](https://github.com/nf-core/tools/pull/3717))
+- Fix paths to logos ([#3715](https://github.com/nf-core/tools/pull/3715))
 - Update test-datasets list subcommand to output plain text urls and paths for easy copying [#3720](https://github.com/nf-core/tools/pull/3720)
 - Remove workflow.trace from nf-test snapshot ([#3721](https://github.com/nf-core/tools/pull/3721))
 - Add GHA to update template nf-test snapshots ([#3723](https://github.com/nf-core/tools/pull/3723))
 - Fix backwards compatibility with python 3.9 in use of Enum ([#3736](https://github.com/nf-core/tools/pull/3736))
 - Fix downloads: temporary files not moved and cleaned up correctly after singularity pull ([#3749](https://github.com/nf-core/tools/pull/3749))
 - impr devcontainer: Add hostRequirements to run with 4CPUs and 16GB ram by default ([#3746](https://github.com/nf-core/tools/pull/3746))
+- Fix diff printing to terminal ([#3759](https://github.com/nf-core/tools/pull/3759))
 - Add .nf-test/ to prettier ignore list ([#3776](https://github.com/nf-core/tools/pull/3776))
+- Update dependency prompt_toolkit to <=3.0.52 ([#3783](https://github.com/nf-core/tools/pull/3783))
+- Update python:3.13-slim Docker digest to 3a6ead7 ([#3786](https://github.com/nf-core/tools/pull/3786))
+- Update dependency textual to v5.3.0 ([#3785](https://github.com/nf-core/tools/pull/3785))
+- update rich-click to 1.9 and use new styling options ([#3787](https://github.com/nf-core/tools/pull/3787))
+- Update pre-commit hook pre-commit/mirrors-mypy to v1.18.2 ([#3792](https://github.com/nf-core/tools/pull/3792))
+- Update python:3.13-slim Docker digest to 5f55cdf ([#3796](https://github.com/nf-core/tools/pull/3796))
+- Update GitHub Actions ([#3795](https://github.com/nf-core/tools/pull/3795))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.13.3 ([#3791](https://github.com/nf-core/tools/pull/3791))
+- Update pre-commit hook pre-commit/pre-commit-hooks to v6 ([#3797](https://github.com/nf-core/tools/pull/3797))
 
 ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08]
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.13-slim@sha256:4c2cf9917bd1cbacc5e9b07320025bdb7cdf2df7b0ceaccb55e9dd7e30987419
+FROM python:3.13-slim@sha256:5f55cdf0c5d9dc1a415637a5ccc4a9e18663ad203673173b8cda8f8dcacef689
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

README.md

@@ -1,7 +1,7 @@
 <h1>
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/docs/images/nfcore-tools_logo_dark.png">
-    <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/docs/images/nfcore-tools_logo_light.png">
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_dark.png">
+    <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_light.png">
   </picture>
 </h1><!-- omit in toc -->