Merge branch 'dev' of https://github.com/nf-core/tools into modules-t…

…emplate-indentation
nf-core · May 6, 2024 · 872d05d · 872d05d
2 parents ac27026 + 2e7ba04
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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
@@ -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.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
@@ -48,14 +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
@@ -61,13 +61,13 @@ 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: |
@@ -158,7 +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
@@ -48,13 +48,13 @@ 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: |
@@ -75,7 +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

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -40,7 +40,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.8", "3.12"]
         runner: ["ubuntu-latest"]
         include:
           - python-version: "3.8"
@@ -61,7 +61,7 @@ jobs:
     name: Get test file matrix
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
       - name: List tests
@@ -87,11 +87,11 @@ jobs:
           cd pytest
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
@@ -143,7 +143,7 @@ jobs:
           fi
 
       - name: Upload coverage
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: coverage_${{ matrix.test }}
           path: .coverage
@@ -158,13 +158,13 @@ jobs:
           mkdir -p pytest
           cd pytest
 
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install dependencies
@@ -177,14 +177,14 @@ jobs:
           mv .github/.coveragerc .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4
       - name: Run coverage
         run: |
           coverage combine --keep coverage*/.coverage*
           coverage report
           coverage xml
 
-      - uses: codecov/codecov-action@54bcd8715eee62d40e33596ef5e8f0f48dbbccab # v4
+      - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be # v4
         with:
           files: coverage.xml
         env:

diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
@@ -6,9 +6,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
       - name: Set up Python
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: 3.x
           cache: pip

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
@@ -44,10 +44,10 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out nf-core/tools
 
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
@@ -56,10 +56,10 @@ jobs:
           path: nf-core/${{ matrix.pipeline }}
           fetch-depth: "0"
 
-      - 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: |
@@ -86,7 +86,7 @@ jobs:
 
       - name: Upload sync log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: sync_log_${{ matrix.pipeline }}
           path: sync_log_${{ matrix.pipeline }}.txt
diff --git a/.github/workflows/update_components_template.yml b/.github/workflows/update_components_template.yml
@@ -11,10 +11,10 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Set up Python
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.x"
 

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: v0.3.3
+    rev: v0.4.3
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -19,7 +19,7 @@ repos:
         alias: ec
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.9.0"
+    rev: "v1.10.0"
     hooks:
       - id: mypy
         additional_dependencies: