Merge branch 'VGP-decontamination' of https://github.com/Delphine-L/iwc…

… into VGP-decontamination

.github/workflows/workflow_test.yml

@@ -11,7 +11,7 @@ jobs:
     with:
       python-version-list: "[\"3.7\"]"
       galaxy-fork: galaxyproject
-      galaxy-branch: release_22.05
+      galaxy-branch: release_23.1
       max-chunks: 4
 
   # Planemo lint the changed repositories
@@ -57,7 +57,7 @@ jobs:
       python-version-list: "[\"3.7\"]"
       repository-list: ${{ needs.setup.outputs.repository-list }}
       galaxy-fork: galaxyproject
-      galaxy-branch: master
+      galaxy-branch: release_23.1
       check-outputs: false
 
   combine_outputs:
@@ -139,3 +139,25 @@ jobs:
          workflows: true
          workflow-namespace: iwc-workflows
          github-token: ${{ secrets.IWC_WORKFLOWS_BOT_TOKEN }}
+
+  deploy-report:
+    name: Report deploy status
+    needs: [deploy]
+    if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }}
+    runs-on: ubuntu-latest
+    steps:
+    # report to the PR if deployment failed
+    - name: Get PR object
+      uses: 8BitJonny/[email protected]
+      id: getpr
+      with:
+        sha: ${{ github.event.after }}
+    - name: Create comment
+      uses: peter-evans/create-or-update-comment@v2
+      with:
+        token: ${{ secrets.PAT }}
+        issue-number: ${{ steps.getpr.outputs.number }}
+        body: |
+          Attention: deployment ${{ needs.deploy.result }}!
+
+          https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}

workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/.dockstore.yml

@@ -0,0 +1,7 @@
+version: 1.2
+workflows:
+- name: main
+  primaryDescriptorPath: /Assembly-Hifi-only-VGP3.ga
+  subclass: Galaxy
+  testParameterFiles:
+  - /Assembly-Hifi-only-VGP3-tests.yml

workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml

@@ -0,0 +1,44 @@
+- doc: Test for Assembly-Hifi-only-VGP3
+  job:
+    Meryl Database:
+      class: File
+      location: https://zenodo.org/record/8371053/files/Meryl-db.meryldb?download=1
+      filetype: meryldb
+    Genomescope Summary:
+      class: File
+      location: https://zenodo.org/record/8371053/files/GenomeScope_Summary.txt?download=1
+      filetype: txt
+    Pacbio Reads Collection:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: yeast_reads_sub1.fastq.gz
+        location: https://zenodo.org/record/8371053/files/yeast_reads_sub1.fastq.gz?download=1
+    Bits for Hifiasm bloom filter: 32
+    SAK input file (Optional): null
+    Name of primary assembly: Primary
+    Name of alternate assembly: Alternate
+  outputs:
+    Hifiasm Primary assembly:
+      asserts:
+        has_n_lines:
+          n: 174
+    Hifiasm Alternate assembly:
+      asserts:
+        has_n_lines:
+          n: 4
+    Assembly Stats on Alternate Assembly:
+      asserts:
+        has_line:
+          line: "# scaffolds	2"
+    Estimated Genome size: 2288021
+    Assembly Stats on Primary assembly:
+      asserts:
+        has_line:
+          line: "# scaffolds	87"
+    Nx Plot:
+      asserts:
+        has_size: 
+          value : 60000
+          delta: 10000