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Merge pull request #73 from nf-core/dsl2
DSL2 conversion
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| @@ -0,0 +1,27 @@ | ||
| root = true | ||
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| [*] | ||
| charset = utf-8 | ||
| end_of_line = lf | ||
| insert_final_newline = true | ||
| trim_trailing_whitespace = true | ||
| indent_size = 4 | ||
| indent_style = space | ||
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| [*.{yml,yaml}] | ||
| indent_size = 2 | ||
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| [*.json] | ||
| insert_final_newline = unset | ||
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| # These files are edited and tested upstream in nf-core/modules | ||
| [/modules/nf-core/**] | ||
| charset = unset | ||
| end_of_line = unset | ||
| insert_final_newline = unset | ||
| trim_trailing_whitespace = unset | ||
| indent_style = unset | ||
| indent_size = unset | ||
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| [/assets/email*] | ||
| indent_size = unset |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,46 +1,34 @@ | ||
| name: nf-core AWS full size tests | ||
| # This workflow is triggered on published releases. | ||
| # It can be additionally triggered manually with GitHub actions workflow dispatch. | ||
| # It can be additionally triggered manually with GitHub actions workflow dispatch button. | ||
| # It runs the -profile 'test_full' on AWS batch | ||
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| on: | ||
| workflow_run: | ||
| workflows: ["nf-core Docker push (release)"] | ||
| types: [completed] | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
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| env: | ||
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | ||
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | ||
| TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }} | ||
| AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }} | ||
| AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }} | ||
| AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }} | ||
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| jobs: | ||
| run-awstest: | ||
| run-tower: | ||
| name: Run AWS full tests | ||
| if: github.repository == 'nf-core/scrnaseq' | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Setup Miniconda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| auto-update-conda: true | ||
| python-version: 3.7 | ||
| - name: Install awscli | ||
| run: conda install -c conda-forge awscli | ||
| - name: Start AWS batch job | ||
| - name: Launch workflow via tower | ||
| uses: nf-core/tower-action@master | ||
| # 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 | ||
| # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command | ||
| run: | | ||
| aws batch submit-job \ | ||
| --region eu-west-1 \ | ||
| --job-name nf-core-scrnaseq \ | ||
| --job-queue $AWS_JOB_QUEUE \ | ||
| --job-definition $AWS_JOB_DEFINITION \ | ||
| --container-overrides '{"command": ["nf-core/scrnaseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/scrnaseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/scrnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' | ||
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| with: | ||
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
| bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }} | ||
| compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} | ||
| pipeline: ${{ github.repository }} | ||
| revision: ${{ github.sha }} | ||
| workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/scrnaseq/work-${{ github.sha }} | ||
| parameters: | | ||
| { | ||
| "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/scrnaseq/results-${{ github.sha }}" | ||
| } | ||
| profiles: '[ "test_full", "aws_tower" ]' | ||
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|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,42 +1,28 @@ | ||
| name: nf-core AWS test | ||
| # This workflow is triggered on push to the master branch. | ||
| # It can be additionally triggered manually with GitHub actions workflow dispatch. | ||
| # It runs the -profile 'test' on AWS batch. | ||
| # This workflow can be triggered manually with the GitHub actions workflow dispatch button. | ||
| # It runs the -profile 'test' on AWS batch | ||
|
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||
| on: | ||
| workflow_dispatch: | ||
|
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||
|
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||
| env: | ||
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | ||
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | ||
| TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }} | ||
| AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }} | ||
| AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }} | ||
| AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }} | ||
|
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||
|
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||
| jobs: | ||
| run-awstest: | ||
| run-tower: | ||
| name: Run AWS tests | ||
| if: github.repository == 'nf-core/scrnaseq' | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Setup Miniconda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| - name: Launch workflow via tower | ||
| uses: nf-core/tower-action@master | ||
|
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||
| with: | ||
| auto-update-conda: true | ||
| python-version: 3.7 | ||
| - name: Install awscli | ||
| run: conda install -c conda-forge awscli | ||
| - name: Start AWS batch job | ||
| # TODO nf-core: You can customise CI pipeline run tests as required | ||
| # For example: adding multiple test runs with different parameters | ||
| # Remember that you can parallelise this by using strategy.matrix | ||
| run: | | ||
| aws batch submit-job \ | ||
| --region eu-west-1 \ | ||
| --job-name nf-core-scrnaseq \ | ||
| --job-queue $AWS_JOB_QUEUE \ | ||
| --job-definition $AWS_JOB_DEFINITION \ | ||
| --container-overrides '{"command": ["nf-core/scrnaseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/scrnaseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/scrnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' | ||
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
| bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }} | ||
| compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} | ||
| pipeline: ${{ github.repository }} | ||
| revision: ${{ github.sha }} | ||
| workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/scrnaseq/work-${{ github.sha }} | ||
| parameters: | | ||
| { | ||
| "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/scrnaseq/results-${{ github.sha }}" | ||
| } | ||
| profiles: '[ "test", "aws_tower" ]' | ||
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