Release 3.0.0

.devcontainer/devcontainer.json

@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

.github/CONTRIBUTING.md

@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-> If you need help using or modifying nf-core/rnafusion then the best place to ask is on the nf-core Slack [#rnafusion](https://nfcore.slack.com/channels/rnafusion) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/rnafusion then the best place to ask is on the nf-core Slack [#rnafusion](https://nfcore.slack.com/channels/rnafusion) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 ## Contribution workflow
 

.github/workflows/awsfulltest.yml

@@ -13,7 +13,7 @@ jobs:
     if: github.repository == 'nf-core/rnafusion'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch build arriba workflow via tower
+      - name: Launch build references workflow via tower
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -28,7 +28,7 @@ jobs:
               "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
               "cosmic_username": "${{ secrets.cosmic_username }}",
               "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
-              "arriba": true,
+              "all": true,
               "build_references": true
             }
           profiles: test_full,aws_tower
@@ -39,7 +39,7 @@ jobs:
             tower_action_*.log
             tower_action_*.json
 
-      - name: Launch arriba workflow via tower
+      - name: Launch run workflow via tower
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -52,223 +52,6 @@ jobs:
               "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
               "cosmic_username": "${{ secrets.cosmic_username }}",
               "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
-              "arriba": true,
+              "all": 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