merging template 2.9

nf-core · Aug 18, 2023 · 0837650 · 0837650
2 parents 1867373 + ada8314
commit 0837650
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diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -13,11 +13,8 @@ jobs:
     if: github.repository == 'nf-core/rnafusion'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
+      - name: Launch build arriba workflow via tower
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -27,13 +24,252 @@ jobs:
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "arriba": true,
+              "build_references": true
             }
-          profiles: test_full
+          profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
+
+      - name: Launch arriba workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "arriba": true,
+            }
+          profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
+
+      - name: Launch build squid workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "squid": true,
+              "build_references": true
+            }
+          profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
+
+      - name: Launch squid workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "squid": true,
+            }
+          profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
+
+      - name: Launch build starfusion workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "starfusion": true,
+              "build_references": true
+            }
+          profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
+
+      - name: Launch starfusion workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "starfusion": true,
+            }
+          profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
+
+      - name: Launch build fusioncatcher workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "fusioncatcher": true,
+              "build_references": true
+            }
+          profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
+
+      - name: Launch fusioncatcher workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "fusioncatcher": true,
+            }
+          profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
+
+      - name: Launch build pizzly workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "pizzly": true,
+              "build_references": true
+            }
+          profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
+
+      - name: Launch pizzly workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "pizzly": true,
+            }
+          profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
 
+      - name: Launch stringtie workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "stringtie": true,
+            }
+          profiles: test_full,aws_tower
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
           path: |
             tower_action_*.log
             tower_action_*.json
+