Merge remote-tracking branch 'upstream/dev' into add-cleanup-to-download

nf-core · Mar 15, 2024 · 6d65c60 · 6d65c60
2 parents 8f3ddb6 + 3fe0a1f
commit 6d65c60
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diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml
@@ -17,7 +17,7 @@ runs:
 
     # Set up Nextflow
     - name: Install Nextflow
-      uses: nf-core/setup-nextflow@v1
+      uses: nf-core/setup-nextflow@v2
       with:
         version: ${{ matrix.NXF_VER }}
 

diff --git a/.github/workflows/changelog.py b/.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)
 

diff --git a/.github/workflows/create-lint-wf.yml b/.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:

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.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@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: latest-everything
 

diff --git a/.github/workflows/create-test-wf.yml b/.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@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: ${{ matrix.NXF_VER }}
 

diff --git a/.github/workflows/pytest.yml b/.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:
@@ -119,32 +121,10 @@ jobs:
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@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: |
@@ -197,7 +177,7 @@ jobs:
           mv .github/.coveragerc .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@87c55149d96e628cc2ef7e6fc2aab372015aec85 # v4
+        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4
       - name: Run coverage
         run: |
           coverage combine --keep coverage*/.coverage*

diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
@@ -15,22 +15,10 @@ jobs:
           cache-dependency-path: setup.py
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@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

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
@@ -67,7 +67,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "latest-everything"
 

diff --git a/.github/workflows/update_components_template.yml b/.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

diff --git a/.gitpod.yml b/.gitpod.yml
@@ -1,4 +1,4 @@
-image: nfcore/gitpod:latest
+image: nfcore/gitpod:dev
 tasks:
   - name: install current state of nf-core/tools and setup pre-commit
     command: |

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.2
+    rev: v0.3.2
     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:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,34 @@
 # nf-core/tools: Changelog
 
+## v2.13.2dev
+
+### Template
+
+- 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))
+
+### 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))
+
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]
 
 ### Template

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.11-slim@sha256:ce81dc539f0aedc9114cae640f8352fad83d37461c24a3615b01f081d0c0583a
+FROM python:3.11-slim@sha256:a2eb07f336e4f194358382611b4fea136c632b40baa6314cb27a366deeaf0144
 LABEL authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for the nfcore tools"
 

diff --git a/docs/api/requirements.txt b/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
diff --git a/nf_core/__init__.py b/nf_core/__init__.py
@@ -1,4 +1,4 @@
-""" Main nf_core module file.
+"""Main nf_core module file.
 
 Shouldn't do much, as everything is under subcommands.
 """

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
-""" nf-core: Helper tools for use with nf-core Nextflow pipelines. """
+"""nf-core: Helper tools for use with nf-core Nextflow pipelines."""
+
 import logging
 import os
 import sys

diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py
@@ -2,7 +2,6 @@
 The ComponentsTest class handles the generation and testing of nf-test snapshots.
 """
 
-
 import logging
 import os
 import re
@@ -91,9 +90,9 @@ def run(self) -> None:
         """Run build steps"""
         self.check_inputs()
         os.environ["NFT_DIFF"] = "pdiff"  # set nf-test differ to pdiff to get a better diff output
-        os.environ[
-            "NFT_DIFF_ARGS"
-        ] = "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
+        os.environ["NFT_DIFF_ARGS"] = (
+            "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
+        )
         with nf_core.utils.set_wd(Path(self.dir)):
             self.check_snapshot_stability()
         if len(self.errors) > 0:

diff --git a/nf_core/components/create.py b/nf_core/components/create.py
@@ -2,7 +2,6 @@
 The ComponentCreate class handles generating of module and subworkflow templates
 """
 
-
 import glob
 import json
 import logging

diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
@@ -3,7 +3,6 @@
 in nf-core pipelines
 """
 
-
 import logging
 import operator
 import os

diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
@@ -1,6 +1,7 @@
 """
 The NFCoreComponent class holds information and utility functions for a single module or subworkflow
 """
+
 import logging
 import re
 from pathlib import Path

diff --git a/nf_core/create.py b/nf_core/create.py
@@ -1,6 +1,7 @@
 """Creates a nf-core pipeline matching the current
 organization's specification based on a template.
 """
+
 import configparser
 import logging
 import os