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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,40 +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 | ||
|
|
||
| on: | ||
| workflow_dispatch: | ||
|
|
||
| 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 }} | ||
|
|
||
| jobs: | ||
| run-awstest: | ||
| run-tower: | ||
| name: Run AWS tests | ||
| if: github.repository == 'nf-core/mhcquant' | ||
| 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@v2 | ||
|
|
||
| # 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-mhcquant \ | ||
| --job-queue $AWS_JOB_QUEUE \ | ||
| --job-definition $AWS_JOB_DEFINITION \ | ||
| --container-overrides '{"command": ["nf-core/mhcquant", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/mhcquant/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/mhcquant/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' | ||
| with: | ||
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | ||
| compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} | ||
| pipeline: ${{ github.repository }} | ||
| revision: ${{ github.sha }} | ||
| workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/mhcquant/work-${{ github.sha }} | ||
| parameters: | | ||
| { | ||
| "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-${{ github.sha }}" | ||
| } | ||
| profiles: test,aws_tower | ||
| pre_run_script: 'export NXF_VER=21.10.3' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/nf-core/mhcquant/master/assets/schema_input.json", | ||
| "title": "nf-core/mhcquant pipeline - params.input schema", | ||
| "description": "Schema for the file provided with params.input", | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "ID": { | ||
| "type": "integer", | ||
| "errorMessage": "Provide an unique identifier for the replicate, must be a numeric value" | ||
| }, | ||
| "Sample": { | ||
| "type": "string", | ||
| "pattern": "^\\S+-?", | ||
| "errorMessage": "Sample name must be provided and cannot contain spaces" | ||
| }, | ||
| "Condition": { | ||
| "type": "string", | ||
| "pattern": "^\\S+-?", | ||
| "errorMessage": "Sample condition must be provided and cannot contain spaces" | ||
| }, | ||
| "ReplicateFileName": { | ||
| "type": "string", | ||
| "errorMessage": "MS file spaces and must have extension '.raw' or '.mzml'", | ||
| "anyOf": [ | ||
| { | ||
| "type": "string", | ||
| "pattern": "^\\S+-?\\.raw$" | ||
| }, | ||
| { | ||
| "type": "string", | ||
| "pattern": "^\\S+-?\\.mzml$" | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
| "required": [ | ||
| "ID", | ||
| "Sample", | ||
| "Condition", | ||
| "ReplicateFileName" | ||
| ] | ||
| } | ||
| } |
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