Merge branch 'dev' into upgrade-to-py3_12

.github/RELEASE_CHECKLIST.md

@@ -3,7 +3,7 @@
 1. Check issue milestones to see outstanding issues to resolve if possible or transfer to the milestones for the next release e.g. [`v1.9`](https://github.com/nf-core/tools/issues?q=is%3Aopen+is%3Aissue+milestone%3A1.9)
 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 tempalte are up to date with the latest releases
+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`.
 6. Make sure all CI tests are passing!
 7. Create a PR from `dev` to `master`

.github/actions/create-lint-wf/action.yml

@@ -17,7 +17,7 @@ runs:
 
  # Set up Nextflow
  - name: Install Nextflow
- uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+ uses: nf-core/setup-nextflow@v2
  with:
  version: ${{ matrix.NXF_VER }}
 

.github/workflows/changelog.py

@@ -79,7 +79,7 @@ def _determine_change_type(pr_title) -> tuple[str, str]:
 section, section_header = _determine_change_type(pr_title)
 
 # Remove section indicator from the PR title.
-pr_title = re.sub(rf"{section}[:\s]*", "", pr_title, flags=re.IGNORECASE)
+pr_title = re.sub(rf"{section}:[\s]*", "", pr_title, flags=re.IGNORECASE)
 
 # Prepare the change log entry.
 pr_link = f"([#{pr_number}]({REPO_URL}/pull/{pr_number}))"
@@ -91,7 +91,6 @@ def _determine_change_type(pr_title) -> tuple[str, str]:
 new_lines = [
  f"- {pr_title} {pr_link}\n",
 ]
-
 print(f"Adding new lines into section '{section}':\n" + "".join(new_lines))
 
 # Finally, updating the changelog.
@@ -144,10 +143,11 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
 
  # Parse version from the line `## v2.12dev` or
  # `## [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]` ...
- if not (m := re.match(r".*(v\d+\.\d+(dev)?).*", line)):
+ if not (m := re.match(r".*(v\d+\.\d+.\d*(dev)?).*", line)):
  print(f"Cannot parse version from line {line.strip()}.", file=sys.stderr)
  sys.exit(1)
  version = m.group(1)
+ print(f"Found version: {version}")
 
  if not inside_version_dev:
  if not version.endswith("dev"):
@@ -209,6 +209,7 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
  # If the line already contains a link to the PR, don't add it again.
  line = _skip_existing_entry_for_this_pr(line, same_section=True)
  section_lines.append(line)
+
  else:
  updated_lines.append(line)
 

.github/workflows/changelog.yml

@@ -4,6 +4,8 @@ on:
  types: [created]
  pull_request_target:
  types: [opened]
+ branches:
+ - dev
 
 jobs:
  update_changelog:

.github/workflows/create-lint-wf.yml

@@ -7,6 +7,9 @@ on:
  - "docs/**"
  - "CHANGELOG.md"
  pull_request:
+ paths-ignore:
+ - "docs/**"
+ - "CHANGELOG.md"
  release:
  types: [published]
  workflow_dispatch:

.github/workflows/create-test-lint-wf-template.yml

@@ -6,6 +6,9 @@ on:
  paths:
  - nf_core/pipeline-template/**
  pull_request:
+ paths-ignore:
+ - "docs/**"
+ - "CHANGELOG.md"
  release:
  types: [published]
  workflow_dispatch:
@@ -72,7 +75,7 @@ jobs:
  pip install .
 
  - name: Install Nextflow
- uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+ uses: nf-core/setup-nextflow@v2
  with:
  version: latest-everything
 

.github/workflows/create-test-wf.yml

@@ -7,6 +7,9 @@ on:
  - "docs/**"
  - "CHANGELOG.md"
  pull_request:
+ paths-ignore:
+ - "docs/**"
+ - "CHANGELOG.md"
  release:
  types: [published]
  workflow_dispatch:
@@ -59,7 +62,7 @@ jobs:
  pip install .
 
  - name: Install Nextflow
- uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+ uses: nf-core/setup-nextflow@v2
  with:
  version: ${{ matrix.NXF_VER }}
 

.github/workflows/pytest.yml

@@ -12,7 +12,9 @@ on:
  paths-ignore:
  - "docs/**"
  - "CHANGELOG.md"
+ # ignore github workflows except for the current one
  - ".github/**"
+ - "!.github/workflows/pytest.yml"
  release:
  types: [published]
  workflow_dispatch:
@@ -108,37 +110,21 @@ jobs:
  sudo add-apt-repository --remove ppa:git-core/ppa
  sudo apt install -y git
 
+ - name: Set up Singularity
+ if: ${{ matrix.test == 'test_download.py'}}
+ uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+ with:
+ singularity-version: 3.8.3
+
  - name: Get current date
  id: date
  run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
  - name: Install Nextflow
- uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
-
- - name: Look if nf-test is already installed and write to env variable
- id: check-nftest
- run: |
- if [ -f /usr/local/bin/nf-test ]; then
- echo "nftest_installed=true" >> $GITHUB_ENV
- else
- echo "nftest_installed=false" >> $GITHUB_ENV
- fi
-
- - name: Cache nf-test installation
- if: env.nftest_installed != 'true'
- id: cache-software
- uses: actions/cache@13aacd865c20de90d75de3b17ebe84f7a17d57d2 # v4
- with:
- path: |
- /usr/local/bin/nf-test
- /home/runner/.nf-test/nf-test.jar
- key: ${{ runner.os }}-nftest-${{ env.date }}
+ uses: nf-core/setup-nextflow@v2
 
  - name: Install nf-test
- if: steps.cache-software.outputs.cache-hit != 'true' && env.nftest_installed != 'true'
- run: |
- wget -qO- https://code.askimed.com/install/nf-test | bash
- sudo mv nf-test /usr/local/bin/
+ uses: nf-core/setup-nf-test@v1
 
  - name: move coveragerc file up
  run: |
@@ -191,14 +177,14 @@ jobs:
  mv .github/.coveragerc .
 
  - name: Download all artifacts
- uses: actions/download-artifact@eaceaf801fd36c7dee90939fad912460b18a1ffe # v4
+ uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4
  - name: Run coverage
  run: |
  coverage combine --keep coverage*/.coverage*
  coverage report
  coverage xml
 
- - uses: codecov/codecov-action@0cfda1dd0a4ad9efc75517f399d859cd1ea4ced1 # v4
+ - uses: codecov/codecov-action@54bcd8715eee62d40e33596ef5e8f0f48dbbccab # v4
  with:
  files: coverage.xml
  env:

.github/workflows/rich-codex.yml

@@ -15,22 +15,10 @@ jobs:
  cache-dependency-path: setup.py
 
  - name: Install Nextflow
- uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
-
- - name: Cache nf-test installation
- id: cache-software
- uses: actions/cache@13aacd865c20de90d75de3b17ebe84f7a17d57d2 # v4
- with:
- path: |
- /usr/local/bin/nf-test
- /home/runner/.nf-test/nf-test.jar
- key: ${{ runner.os }}-nftest-${{ env.date }}
+ uses: nf-core/setup-nextflow@v2
 
  - name: Install nf-test
- if: steps.cache-software.outputs.cache-hit != 'true'
- run: |
- wget -qO- https://code.askimed.com/install/nf-test | bash
- sudo mv nf-test /usr/local/bin/
+ uses: nf-core/setup-nf-test@v1
 
  - name: Install nf-core/tools
  run: pip install git+https://github.com/nf-core/tools.git@dev

.github/workflows/sync.yml

@@ -67,7 +67,7 @@ jobs:
  pip install .
 
  - name: Install Nextflow
- uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+ uses: nf-core/setup-nextflow@v2
  with:
  version: "latest-everything"
 

.github/workflows/update_components_template.yml

@@ -23,11 +23,11 @@ jobs:
 
  - name: Update modules
  run: nf-core modules update --all
- working-directory: nf-core/pipeline-template
+ working-directory: nf_core/pipeline-template
 
  - name: Update subworkflows
  run: nf-core subworkflows update --all
- working-directory: nf-core/pipeline-template
+ working-directory: nf_core/pipeline-template
 
  # Commit the changes
  - name: Commit changes

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
  - repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.2.2
+ rev: v0.3.3
  hooks:
  - id: ruff # linter
  args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -9,6 +9,8 @@ repos:
  rev: "v3.1.0"
  hooks:
  - id: prettier
+ additional_dependencies:
+ - prettier@3.2.5
 
  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
  rev: "2.7.3"
@@ -17,7 +19,7 @@ repos:
  alias: ec
 
  - repo: https://github.com/pre-commit/mirrors-mypy
- rev: "v1.8.0"
+ rev: "v1.9.0"
  hooks:
  - id: mypy
  additional_dependencies:

CHANGELOG.md

@@ -1,19 +1,58 @@
 # nf-core/tools: Changelog
 
-## v3.0dev
+## v2.13.2dev
 
 ### Template
 
-- Remove obsolete editor settings in `devcontainer.json` and `gitpod.yml` ([#2795](https://github.com/nf-core/tools/pull/2795))
+- Remove fasta default from nextflow.config ([#2828](https://github.com/nf-core/tools/pull/2828))
+- Update templates to use nf-core/setup-nextflow v2
+- Link to troubleshooting docs when pipeline fails ([#2845](https://github.com/nf-core/tools/pull/2845))
+- Add fallback to `download_pipeline.yml` in case the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846))
+- Set topic variable correctly in the mastodon announcement ([#2848](https://github.com/nf-core/tools/pull/2848))
+- Add a cleanup action to `download_pipeline.yml` to fix failures caused by inadequate storage space on the runner ([#2849](https://github.com/nf-core/tools/pull/2849))
 - Update python to 3.12 ([#2805](https://github.com/nf-core/tools/pull/2805))
 
 ### Linting
 
+- Only match assignments of params in `main.nf` and not references like `params.aligner == <something>` ([#2833](https://github.com/nf-core/tools/pull/2833))
+
+### Components
+
+### General
+
+- Update CI to use nf-core/setup-nextflow v2
+- Changelog bot: handle also patch version before dev suffix ([#2820](https://github.com/nf-core/tools/pull/2820))
+- Fix path in component update script ([#2823](https://github.com/nf-core/tools/pull/2823))
+- Update prettier to 3.2.5 ([#2830](https://github.com/nf-core/tools/pull/2830))
+- Update GitHub Actions ([#2827](https://github.com/nf-core/tools/pull/2827))
+- Switch to setup-nf-test ([#2834](https://github.com/nf-core/tools/pull/2834))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.3.2 ([#2836](https://github.com/nf-core/tools/pull/2836))
+- Add tests for assignment and referencing of params in main.nf ([#2841](https://github.com/nf-core/tools/pull/2841))
+- Optimize layers in dockerfile ([#2842](https://github.com/nf-core/tools/pull/2842))
+- Update gitpod/workspace-base Docker digest to 1e133e5 ([#2843](https://github.com/nf-core/tools/pull/2843))
+- Update python:3.11-slim Docker digest to a2eb07f ([#2847](https://github.com/nf-core/tools/pull/2847))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.3.3 ([#2850](https://github.com/nf-core/tools/pull/2850))
+
+## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]
+
+### Template
+
+- Remove obsolete editor settings in `devcontainer.json` and `gitpod.yml` ([#2795](https://github.com/nf-core/tools/pull/2795))
+- Add nf-test test instructions to contributing and PR template ([#2807](https://github.com/nf-core/tools/pull/2807))
+- Fix topic extraction step for hashtags in toots ([#2810](https://github.com/nf-core/tools/pull/2810))
+- Update modules and subworkflows in the template ([#2811](https://github.com/nf-core/tools/pull/2811))
+- Unpin setup-nextflow and action-tower-launch ([#2806](https://github.com/nf-core/tools/pull/2806))
+
+### Download
+
+- Improved offline container image resolution by introducing symlinks, fixes issues [#2751](https://github.com/nf-core/tools/issues/2751), [#2644](https://github.com/nf-core/tools/issues/2644) and [demultiplex#164](https://github.com/nf-core/demultiplex/issues/164): ([#2768](https://github.com/nf-core/tools/pull/2768))
+
+### Linting
+
 ### Components
 
 ### General
 
-- chore(deps): update seqeralabs/action-tower-launch digest to aa88624 ([#2793](https://github.com/nf-core/tools/pull/2793))
 - chore(deps): update codecov/codecov-action digest to 0cfda1d ([#2794](https://github.com/nf-core/tools/pull/2794))
 - chore(deps): update gitpod/workspace-base docker digest to c15ee2f ([#2799](https://github.com/nf-core/tools/pull/2799))
 
@@ -43,6 +82,8 @@
 - Patch: handle file not found when it is an added file to a module ([#2771](https://github.com/nf-core/tools/pull/2771))
 - Handle symlinks when migrating pytest ([#2770](https://github.com/nf-core/tools/pull/2770))
 - Add `--profile` parameter to nf-test command ([#2767](https://github.com/nf-core/tools/pull/2767))
+- Reduce the sha length in the `nf-core modules list local` and add links to the specific commit ([#2870](https://github.com/nf-core/tools/pull/2870))
+- Add links the nf-core module page and to open the local file in VSCode for module lint results ([#2870](https://github.com/nf-core/tools/pull/2870))
 
 ### General
 

Dockerfile

@@ -1,6 +1,6 @@
 FROM python:3.12-slim
-LABEL authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \
- description="Docker image containing requirements for the nfcore tools"
+LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
+ description="Docker image containing requirements for nf-core/tools"
 
 # Do not pick up python packages from $HOME
 ENV PYTHONNUSERSITE=1

docs/api/requirements.txt

@@ -1,4 +1,5 @@
 Sphinx>=3.3.1
 sphinxcontrib-napoleon
+sphinx-markdown-builder
 sphinx_rtd_theme>=0.5.0
 myst-parser