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Merge pull request #320 from nf-core/dev
Release 2.2.0
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‎.devcontainer/devcontainer.json‎

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{
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"name": "nfcore",
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"image": "nfcore/gitpod:latest",
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"remoteUser": "gitpod",
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// Configure tool-specific properties.
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"customizations": {
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// Configure properties specific to VS Code.
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"vscode": {
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"python.defaultInterpreterPath": "/opt/conda/bin/python",
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"python.linting.enabled": true,
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"python.linting.pylintEnabled": true,
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"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
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"python.formatting.yapfPath": "/opt/conda/bin/yapf",
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"python.linting.flake8Path": "/opt/conda/bin/flake8",
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"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
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"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
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"python.linting.pylintPath": "/opt/conda/bin/pylint"
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},
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
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}
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}
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}

‎.editorconfig‎

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indent_size = 4
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indent_style = space
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[*.{md,yml,yaml,html,css,scss,js}]
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[*.{md,yml,yaml,html,css,scss,js,cff}]
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indent_size = 2
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# These files are edited and tested upstream in nf-core/modules

‎.gitattributes‎

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*.config linguist-language=nextflow
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*.nf.test linguist-language=nextflow
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modules/nf-core/** linguist-generated
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subworkflows/nf-core/** linguist-generated

‎.github/CONTRIBUTING.md‎

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### Images and figures
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For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
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## GitHub Codespaces
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This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
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To get started:
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- Open the repo in [Codespaces](https://github.com/nf-core/rnafusion/codespaces)
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- Tools installed
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- nf-core
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- Nextflow
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Devcontainer specs:
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- [DevContainer config](.devcontainer/devcontainer.json)
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- [Dockerfile](.devcontainer/Dockerfile)

‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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attributes:
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label: System information
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description: |
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* Nextflow version _(eg. 21.10.3)_
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* Nextflow version _(eg. 22.10.1)_
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* Hardware _(eg. HPC, Desktop, Cloud)_
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* Executor _(eg. slurm, local, awsbatch)_
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* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_

‎.github/PULL_REQUEST_TEMPLATE.md‎

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- [ ] This comment contains a description of changes (with reason).
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- [ ] If you've fixed a bug or added code that should be tested, add tests!
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnafusion/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, also make a PR on the nf-core/rnafusion _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnafusion/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/rnafusion _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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- [ ] Make sure your code lints (`nf-core lint`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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- [ ] Usage Documentation in `docs/usage.md` is updated.

‎.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 workflow via tower
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- name: Launch build arriba workflow via tower
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uses: nf-core/tower-action@v3
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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workdir: s3://${{ 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-${{ github.sha }}"
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"outdir": "s3://${{ 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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"arriba": true,
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"build_references": true
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}
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profiles: test_full_build,aws_tower
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nextflow_config: |
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process.errorStrategy = 'retry'
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process.maxRetries = 3
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- name: Launch workflow via tower
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profiles: test_full,aws_tower
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- name: Launch arriba workflow via tower
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uses: nf-core/tower-action@v3
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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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"arriba": true,
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}
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profiles: test_full,aws_tower
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- name: Launch build squid workflow via tower
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uses: nf-core/tower-action@v3
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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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- name: Launch squid workflow via tower
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uses: nf-core/tower-action@v3
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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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- name: Launch build starfusion workflow via tower
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uses: nf-core/tower-action@v3
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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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- name: Launch starfusion workflow via tower
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uses: nf-core/tower-action@v3
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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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- name: Launch build fusioncatcher workflow via tower
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uses: nf-core/tower-action@v3
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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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- name: Launch fusioncatcher workflow via tower
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uses: nf-core/tower-action@v3
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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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- name: Launch build pizzly workflow via tower
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uses: nf-core/tower-action@v3
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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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- name: Launch pizzly workflow via tower
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uses: nf-core/tower-action@v3
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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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- name: Launch stringtie workflow via tower
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uses: nf-core/tower-action@v3
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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workdir: s3://${{ 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-${{ github.sha }}"
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"outdir": "s3://${{ 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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