Merge branch 'galaxyproject:main' into treevalgal

Delphine-L · Oct 10, 2024 · bd88b4a · bd88b4a
2 parents 301119a + fabc844
commit bd88b4a
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Showing 106 changed files with 7,113 additions and 2,160 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -27,7 +27,7 @@ jobs:
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-workflow-tests' }}
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -43,11 +43,11 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -56,7 +56,7 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -85,14 +85,14 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -105,6 +105,7 @@ jobs:
         mode: lint
         workflows: true
         repository-list: "${{ needs.setup.outputs.repository-list }}"
+        additional-planemo-options: --iwc
 
   test:
     name: Test workflows
@@ -129,14 +130,14 @@ jobs:
     steps:
     # checkout the repository
     # and use it as the current working directory
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -153,7 +154,7 @@ jobs:
         galaxy-branch: ${{ needs.setup.outputs.branch }}
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Workflow test output ${{ matrix.chunk }}'
         path: upload
@@ -172,14 +173,14 @@ jobs:
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -190,7 +191,7 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All workflow test results'
         path: upload
@@ -201,7 +202,7 @@ jobs:
 
     - name: Create comment
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-workflow-tests' }}
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}

diff --git a/.github/workflows/enable_ci_workflows.yml b/.github/workflows/enable_ci_workflows.yml
@@ -8,7 +8,7 @@ jobs:
     name: Enable CI workflows
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - name: run Python script

diff --git a/.github/workflows/setup.yml b/.github/workflows/setup.yml
@@ -60,17 +60,17 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ inputs.galaxy-fork }}/galaxy refs/heads/${{ inputs.galaxy-branch }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
     - name: Cache .planemo
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-planemo
       with:
         path: ~/.planemo
@@ -79,7 +79,7 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks

diff --git a/.github/workflows/slash.yaml b/.github/workflows/slash.yaml
@@ -8,7 +8,7 @@ jobs:
     steps:
       - name: Slash Command Dispatch
         if: github.repository_owner == 'galaxyproject'
-        uses: peter-evans/slash-command-dispatch@v3
+        uses: peter-evans/slash-command-dispatch@v4
         with:
           token: ${{ secrets.PAT }}
           commands: |

diff --git a/.github/workflows/test_workflows.yml b/.github/workflows/test_workflows.yml
@@ -60,18 +60,20 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ inputs.galaxy-head-sha }}
+    - name: Clean dotnet folder for space
+      run: rm -Rf /usr/share/dotnet
     - name: Planemo test workflows
       uses: galaxyproject/planemo-ci-action@v1
       id: test-workflows
@@ -84,7 +86,7 @@ jobs:
         galaxy-branch: ${{ inputs.galaxy-branch }}
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ inputs.chunk-count }}
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Workflow test output ${{ matrix.chunk }}'
         path: upload

diff --git a/.github/workflows/usegalaxy-star-installation.yml b/.github/workflows/usegalaxy-star-installation.yml
@@ -9,9 +9,9 @@ jobs:
   workflow-install:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Cache downloads
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             ~/.cache/pip

diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml
@@ -24,14 +24,14 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -44,6 +44,7 @@ jobs:
         mode: lint
         workflows: true
         repository-list: "${{ needs.setup.outputs.repository-list }}"
+        additional-planemo-options: --iwc
 
   test:
     name: Test workflows
@@ -69,14 +70,14 @@ jobs:
         python-version: ['3.11']
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -94,7 +95,7 @@ jobs:
     - name: Debug PR number
       run: |
           cat ./upload/NR
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload
@@ -114,14 +115,14 @@ jobs:
     runs-on: ubuntu-latest
     if: github.ref == 'refs/heads/main' && github.repository_owner == 'galaxyproject'
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -155,12 +156,12 @@ jobs:
     steps:
     # report to the PR if deployment failed
     - name: Get PR object
-      uses: 8BitJonny/gh-get-current-pr@2.2.0
+      uses: 8BitJonny/gh-get-current-pr@3.0.0
       id: getpr
       with:
         sha: ${{ github.event.after }}
     - name: Create comment
-      uses: peter-evans/create-or-update-comment@v3
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         issue-number: ${{ steps.getpr.outputs.number }}

diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,3 @@
 tool_test_output.html
 tool_test_output.json
+.DS_Store
diff --git a/...s/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml b/...s/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml
@@ -32,6 +32,7 @@
     Name for Haplotype 1: Hap1
     Name for Haplotype 2: Hap2
     Homozygous Read Coverage: null
+    Database for Busco Lineage: v5
   outputs:
     Hifiasm HiC hap1:
       assert: