Merge pull request #288 from drpatelh/fixes

Update Github Action to run full-sized test for all 3 download methods
nf-core · Feb 22, 2024 · dc7c39d · dc7c39d
2 parents 33df093 + 2263d70
commit dc7c39d
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Showing 2 changed files with 19 additions and 6 deletions.
diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
@@ -19,20 +19,24 @@ jobs:
   run-full-tests-on-aws:
     if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' || !github.event.inputs }}
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        download_method: ["aspera", "ftp", "sratools"]
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
-          run_name: "aws_fetchngs_full"
+          run_name: "aws_fetchngs_full_${{ matrix.download_method }}"
           revision: ${{ github.sha }}
           profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-${{ github.sha }}/"
+                "download_method": "${{ matrix.download_method }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-${{ github.sha }}/download_method_${{ matrix.download_method }}/"
             }
       - uses: actions/upload-artifact@v3
         with:
@@ -42,20 +46,24 @@ jobs:
   run-full-tests-on-azure:
     if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        download_method: ["aspera", "ftp", "sratools"]
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/fetchngs/work-${{ github.sha }}"
-          run_name: "azure_fetchngs_full"
+          run_name: "azure_fetchngs_full_${{ matrix.download_method }}"
           revision: ${{ github.sha }}
           profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-${{ github.sha }}/"
+                "download_method": "${{ matrix.download_method }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-${{ github.sha }}/download_method_${{ matrix.download_method }}/"
             }
       - uses: actions/upload-artifact@v3
         with:
@@ -65,20 +73,24 @@ jobs:
   run-full-tests-on-gcp:
     if: ${{ github.event.inputs.platform == 'gcp' || !github.event.inputs }}
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        download_method: ["aspera", "ftp", "sratools"]
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/fetchngs/work-${{ github.sha }}"
-          run_name: "gcp_fetchngs_full"
+          run_name: "gcp_fetchngs_full_${{ matrix.download_method }}"
           revision: ${{ github.sha }}
           profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-${{ github.sha }}/"
+                "download_method": "${{ matrix.download_method }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-${{ github.sha }}/download_method_${{ matrix.download_method }}/"
             }
       - uses: actions/upload-artifact@v3
         with:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -48,6 +48,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #268](https://github.com/nf-core/fetchngs/pull/268) - Add mermaid diagram
 - [PR #273](https://github.com/nf-core/fetchngs/pull/273) - Update utility subworkflows
 - [PR #283](https://github.com/nf-core/fetchngs/pull/283) - Template update for nf-core/tools v2.13
+- [PR #288](https://github.com/nf-core/fetchngs/pull/288) - Update Github Action to run full-sized test for all 3 download methods
 - [PR #290](https://github.com/nf-core/fetchngs/pull/290) - Remove mentions of deprecated Synapse functionality in pipeline
 
 ### Software dependencies