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Merge pull request #447 from nf-core/dev
Release 3.0.0
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‎.devcontainer/devcontainer.json‎

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

‎.github/CONTRIBUTING.md‎

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@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
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However, don't be put off by this template - other more general issues and suggestions are welcome!
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Contributions to the code are even more welcome ;)
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> 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)).
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:::info
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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)).
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:::
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## Contribution workflow
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‎.github/workflows/awsfulltest.yml‎

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if: github.repository == 'nf-core/rnafusion'
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runs-on: ubuntu-latest
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steps:
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- name: Launch build arriba workflow via tower
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- name: Launch build references workflow via tower
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
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"cosmic_username": "${{ secrets.cosmic_username }}",
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"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
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"arriba": true,
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"all": true,
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"build_references": true
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}
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profiles: test_full,aws_tower
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tower_action_*.log
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tower_action_*.json
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- name: Launch arriba workflow via tower
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- name: Launch run workflow via tower
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
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"cosmic_username": "${{ secrets.cosmic_username }}",
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"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
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"arriba": true,
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"all": true,
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}
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profiles: test_full,aws_tower
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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- name: Launch build squid workflow via tower
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
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"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
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"cosmic_username": "${{ secrets.cosmic_username }}",
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"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
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"squid": true,
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"build_references": true
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}
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profiles: test_full,aws_tower
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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- name: Launch squid workflow via tower
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
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"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
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"cosmic_username": "${{ secrets.cosmic_username }}",
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"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
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"squid": true,
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}
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profiles: test_full,aws_tower
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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- name: Launch build starfusion workflow via tower
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
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"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
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"cosmic_username": "${{ secrets.cosmic_username }}",
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"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
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"starfusion": true,
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"build_references": true
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}
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profiles: test_full,aws_tower
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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- name: Launch starfusion workflow via tower
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
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"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
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"cosmic_username": "${{ secrets.cosmic_username }}",
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"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
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"starfusion": true,
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}
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profiles: test_full,aws_tower
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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- name: Launch build fusioncatcher workflow via tower
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
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"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
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"cosmic_username": "${{ secrets.cosmic_username }}",
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"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
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"fusioncatcher": true,
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"build_references": true
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}
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profiles: test_full,aws_tower
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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- name: Launch fusioncatcher workflow via tower
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
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"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
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"cosmic_username": "${{ secrets.cosmic_username }}",
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"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
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"fusioncatcher": true,
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}
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profiles: test_full,aws_tower
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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- name: Launch build pizzly workflow via tower
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
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"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
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"cosmic_username": "${{ secrets.cosmic_username }}",
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"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
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"pizzly": true,
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"build_references": true
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}
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profiles: test_full,aws_tower
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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- name: Launch pizzly workflow via tower
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
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"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
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"cosmic_username": "${{ secrets.cosmic_username }}",
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"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
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"pizzly": true,
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}
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profiles: test_full,aws_tower
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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- name: Launch stringtie workflow via tower
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
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"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
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"cosmic_username": "${{ secrets.cosmic_username }}",
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"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
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"stringtie": true,
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}
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profiles: test_full,aws_tower
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json

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