Merge pull request #2958 from nf-core/dev

Dev -> Master for 2.14.0
nf-core · May 8, 2024 · 671e1df · 671e1df
2 parents 9eac5e9 + 293c781
commit 671e1df
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -37,5 +37,5 @@ body:
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of nf-core/tools _(eg. 1.1, 1.5, 1.8.2)_
-        * Python version _(eg. 3.10, 3.11)_
+        * Version of nf-core/tools _(eg. 1.10, 1.12.1, 1.13)_
+        * Python version _(eg. 3.11, 3.12)_
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 }}
 
@@ -77,7 +77,7 @@ runs:
 
     - name: Upload log file artifact
       if: ${{ always() }}
-      uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+      uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
       with:
         name: nf-core-log-file-${{ matrix.NXF_VER }}
         path: create-lint-wf/log.txt

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/changelog.yml b/.github/workflows/changelog.yml
@@ -19,7 +19,7 @@ jobs:
       )
 
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 
@@ -36,9 +36,9 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install packages
         run: |
@@ -64,10 +64,10 @@ jobs:
           git diff --exit-code ${GITHUB_WORKSPACE}/CHANGELOG.md || echo "changed=YES" >> $GITHUB_ENV
           echo "File changed: ${{ env.changed }}"
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install pre-commit

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:
@@ -45,14 +48,14 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: pip
 
       - name: Install python dependencies

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:
@@ -58,21 +61,21 @@ jobs:
           cd create-lint-wf-template
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install python dependencies
         run: |
           python -m pip install --upgrade pip
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: latest-everything
 
@@ -155,7 +158,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: nf-core-log-file-${{ matrix.TEMPLATE }}
           path: create-test-lint-wf/artifact_files.tar

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:
@@ -45,21 +48,21 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install python dependencies
         run: |
           python -m pip install --upgrade pip
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: ${{ matrix.NXF_VER }}
 
@@ -72,7 +75,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: nf-core-log-file-${{ matrix.NXF_VER }}
           path: create-test-wf/log.txt

diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install python dependencies
         run: |

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
@@ -18,12 +18,12 @@ jobs:
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install pre-commit

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev

diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest