Merge branch 'dev' into issues/3751-codespaces-badge

Author: mirpedrol

.devcontainer/build-devcontainer/Dockerfile

@@ -5,10 +5,10 @@ FROM "mcr.microsoft.com/devcontainers/miniconda@sha256:8e262a2664fab1d53054738d3
 # copy this repo at current revision
 COPY . /root/nfcore-tools/
 
-# Explicitly reinstall python 3.14 via conda
+# Explicitly reinstall python 3.13 via conda
 # install local nf-core tools version, and precommit hooks
 RUN cd /root/nfcore-tools/ && \
-    conda install -y python=3.14 && \
+    conda install -y python=3.13 && \
     pip install --no-cache-dir --upgrade pip setuptools wheel pre-commit && \
     pip install -r requirements.txt --no-cache-dir -e . && \
     pre-commit install --install-hooks && \

.github/RELEASE_CHECKLIST.md

@@ -4,7 +4,7 @@
 2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
 3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
 4. Check that modules/subworkflows in template are up to date with the latest releases
-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`.
+5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the `.devcontainer/devcontainer.json` container to `nfcore/gitpod:latest`.
 6. Make sure all CI tests are passing!
 7. Create a PR from `dev` to `main`
 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.
@@ -22,4 +22,4 @@
 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`.
+6. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the `.devcontainer/devcontainer.json` container to `nfcore/gitpod:dev`.

CHANGELOG.md

@@ -1,6 +1,19 @@
 # nf-core/tools: Changelog
 
-## v3.4.0dev
+## [v3.4.1 - Ducol Dingo Patch 1](https://github.com/nf-core/tools/releases/tag/3.4.0) - [2025-10-10]
+
+### Template
+
+- Fix devcontainer configuration for pipeline template ([#3835](https://github.com/nf-core/tools/pull/3835))
+- Fix Jinja2 template formatting in nextflow.config ([#3836](https://github.com/nf-core/tools/pull/3836))
+- Add codespaces badge to template README ([#3824](https://github.com/nf-core/tools/pull/3824))
+
+## [v3.4.0 - Ducol Dingo](https://github.com/nf-core/tools/releases/tag/3.4.0) - [2025-10-10]
+
+**Highlights**
+
+- Bumping minimum Nextflow version to 25.04.0.
+- Refactoring of the `nf-core pipelines download` command.
 
 ### Template
 
@@ -11,26 +24,27 @@
 - 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))
+- Add NXF_VERSION environment variable to nf-test workflow ([#3770](https://github.com/nf-core/tools/pull/3770))
+- 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))
-- feat: Add codespaces badge to template README ([#3824](https://github.com/nf-core/tools/pull/3824))
+- update pipeline template subworkflows ([#3826](https://github.com/nf-core/tools/pull/3826))
+- fix AWS tests launch action ([#3827](https://github.com/nf-core/tools/pull/3827))
 
 ### Linting
 
-- Add .nf-test folder to prettierignore list ([#3625](https://github.com/nf-core/tools/pull/3625))
 - 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))
 - Linting of patched subworkflows ([#3755](https://github.com/nf-core/tools/pull/3755))
 - Add link to modules and subworkflows linting error docs ([#3818](https://github.com/nf-core/tools/pull/3818))
+- fix ternary container linting ([#3830](https://github.com/nf-core/tools/pull/3830))
 
 ### 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))
+- nf-core modules bump-version supports specifying the toolkit ([#3608](https://github.com/nf-core/tools/pull/3608))
 - use same logic for super-tool selection in modules lint and bump-version ([#3823](https://github.com/nf-core/tools/pull/3823))
 - Override example keywords in modules test ([#3801](https://github.com/nf-core/tools/pull/3801))
 - update test assertions in modules template to current recommendations and remove `single_end` from example meta value ([#3815](https://github.com/nf-core/tools/pull/3815))
@@ -42,23 +56,16 @@
 ### General
 
 - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674))
-- Update marocchino/sticky-pull-request-comment digest to 7737449 ([#3681](https://github.com/nf-core/tools/pull/3681))
 - Stop using Gitpod in favor of devcontainer for codespaces ([#3569](https://github.com/nf-core/tools/pull/3569))
-- Update dependency textual to v5 ([#3699](https://github.com/nf-core/tools/pull/3699))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.7 ([#3697](https://github.com/nf-core/tools/pull/3697))
-- Update pre-commit hook pre-commit/mirrors-mypy to v1.17.1 ([#3698](https://github.com/nf-core/tools/pull/3698))
-- Update python:3.13-slim Docker digest to 4c2cf99 ([#3700](https://github.com/nf-core/tools/pull/3700))
 - Validation of meta.yaml in cross-org repos ([#3680](https://github.com/nf-core/tools/pull/3680))
 - Refactor downloads command ([#3634](https://github.com/nf-core/tools/pull/3634))
   - Split `download.py` into subdirectory `download/`
   - Use `nextflow inspect` for container discovery and remove legacy regex container discovery (requires Nextflow >= 25.04.04)
   - Add support for downloading docker images into tar archives
-  - Change long flag `--parallel-downloads` to `--parallel`. Short flag remains `-d`.
   - Add pipeline to test data to be compatible with `nextflow inspect`
 - 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))
@@ -69,18 +76,23 @@
 - Fix Issues/3729: Remove temporary folders created from nextflow inspect during downloads ([#3750](https://github.com/nf-core/tools/pull/3750))
 - 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))
+- pipelines bump-version: fix indentation for list in dumped .nf-core.yml ([#3829](https://github.com/nf-core/tools/pull/3829))
+
+### Version updates
+
+- Update marocchino/sticky-pull-request-comment digest to 7737449 ([#3681](https://github.com/nf-core/tools/pull/3681))
+- Update codecov/codecov-action digest to fdcc847 ([#3717](https://github.com/nf-core/tools/pull/3717))
 - 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 dependency textual to v6 ([#3793](https://github.com/nf-core/tools/pull/3793))
 - 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))
 - Update dependency python to 3.14 ([#3817](https://github.com/nf-core/tools/pull/3817))
 - update Dockerfile to python 3.14 ([#3822](https://github.com/nf-core/tools/pull/3822))
+- downgrade python version to 3.13 in devcontainer ([#3834](https://github.com/nf-core/tools/pull/3834))
+- Update GitHub Actions ([#3795](https://github.com/nf-core/tools/pull/3795))
 
 ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08]
 

nf_core/modules/lint/main_nf.py

@@ -314,11 +314,11 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
     # Deprecated enable_conda
     for i, raw_line in enumerate(lines):
         url = None
-        line = raw_line.strip(" \n'\"}:")
+        line = raw_line.strip(" \n'\"}:?")
 
         # Catch preceding "container "
         if line.startswith("container"):
-            line = line.replace("container", "").strip(" \n'\"}:")
+            line = line.replace("container", "").strip(" \n'\"}:?")
 
         if _container_type(line) == "conda":
             if "bioconda::" in line:
@@ -592,7 +592,7 @@ def check_process_labels(self, lines):
 def check_container_link_line(self, raw_line, registry):
     """Look for common problems in the container name / URL, for docker and singularity."""
 
-    line = raw_line.strip(" \n'\"}:")
+    line = raw_line.strip(" \n'\"}:?")
 
     # lint double quotes
     if line.count('"') > 2:

nf_core/pipeline-template/.devcontainer/devcontainer.json

@@ -5,7 +5,16 @@
     "remoteUser": "root",
     "privileged": true,
 
-    // Mount full current path to make mounting into docker-outside-of-docker work
-    "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
-    "workspaceFolder": "${localWorkspaceFolder}"
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
+    }
 }

nf_core/pipeline-template/.devcontainer/setup.sh

@@ -1,4 +1,13 @@
 #!/usr/bin/env bash
 
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PROMPT_DIRTRIM=2
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
 # Update welcome message
 echo "Welcome to the {{ name }} devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -28,21 +28,21 @@ jobs:
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ steps.revision.outputs.revision }}{% endraw %}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ steps.revision.outputs.revision }}{% endraw %}
           parameters: |
             {
               "hook_url": "{% raw %}${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}{% endraw %}",
-              "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ steps.revision.outputs.revision }}{% endraw %}"
+              "outdir": "s3://{% raw %}${{ vars.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ steps.revision.outputs.revision }}{% endraw %}"
             }
           profiles: test_full
 
       - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json

nf_core/pipeline-template/.github/workflows/awstest.yml

@@ -14,20 +14,20 @@ jobs:
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {
-              "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-test-${{ github.sha }}{% endraw %}"
+              "outdir": "s3://{% raw %}${{ vars.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-test-${{ github.sha }}{% endraw %}"
             }
           profiles: test
 
       - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json

nf_core/pipeline-template/.prettierignore

@@ -20,4 +20,3 @@ bin/
 {%- if rocrate %}
 ro-crate-metadata.json
 {%- endif %}
-.nf-test/

nf_core/pipeline-template/modules.json

@@ -23,12 +23,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {