name: AWS Megatests
# This workflow is triggered on PRs to the master branch.
# It runs the -profile 'test' on AWS batch

on:
  pull_request:
    branches:
    - 'master'
  release:
    types: [published]

jobs:
  run-awstest:
    name: Run AWS test
    runs-on: ubuntu-latest
    steps:
      - name: Setup Miniconda
        uses: goanpeca/setup-miniconda@v1.0.2
        with:
          auto-update-conda: true
          python-version: 3.7
      - name: Install awscli
        run: conda install -c conda-forge awscli
      - name: Start AWS batch job
        env:
          AWS_ACCESS_KEY_ID: ${{secrets.AWS_KEY_ID}}
          AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_KEY_SECRET}}
          TOWER_ACCESS_TOKEN: ${{secrets.TOWER_ACCESS_TOKEN}}
        run: |
          aws batch submit-job --region eu-west-1 --job-name nf-core-sarek --job-queue 'default-8b3836e0-5eda-11ea-96e5-0a2c3f6a2a32' --job-definition nextflow --container-overrides command=nf-core/sarek,"-r ${GITHUB_SHA} -profile test --outdir s3://nf-core-awsmegatests/sarek/results-${GITHUB_SHA} -w s3://nf-core-awsmegatests/sarek/work-${GITHUB_SHA}" 

name: AWS Megatests
# This workflow is triggered on PRs to the master branch.
# It runs the -profile 'test' on AWS batch

on:
  pull_request:
    branches:
    - master
  release:
    types: [published]

jobs:
  run-awstest:
    name: Run AWS test
    runs-on: ubuntu-latest
    steps:
      - name: Setup Miniconda
        uses: goanpeca/setup-miniconda@v1.0.2
        with:
          auto-update-conda: true
          python-version: 3.7
      - name: Install awscli
        run: conda install -c conda-forge awscli
      - name: Start AWS batch job
        env:
          AWS_ACCESS_KEY_ID: ${{secrets.AWS_KEY_ID}}
          AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_KEY_SECRET}}
          TOWER_ACCESS_TOKEN: ${{secrets.TOWER_ACCESS_TOKEN}}
        run: |
          aws batch submit-job --region eu-west-1 --job-name nf-core-sarek --job-queue 'default-8b3836e0-5eda-11ea-96e5-0a2c3f6a2a32' --job-definition nextflow --container-overrides '{"command": ["nf-core/sarek", "-r ${GITHUB_SHA} -profile test --outdir s3://nf-core-awsmegatests/sarek/results-${GITHUB_SHA} -w s3://nf-core-awsmegatests/sarek/work-${GITHUB_SHA} -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' 

Add nextflow tower properly as suggested
Add nextflow tower properly as suggested
