WorkflowMicrobiomeCore/streamflowMain.yml at main · qBioTurin/WorkflowMicrobiomeCore · GitHub

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#!/usr/bin/env streamflow
version: v1.0
workflows:
  workflow:
    type: cwl
    config:
      file: ./main.cwl
      settings: config.yml
      docker:
        - step: /
          deployment:
            type: none
            config: {}
    bindings:
      - step: /wrapperCore/genomemapper
        target:
          deployment: c3sfr1-slurm
          service: genomemapper
      - step: /wrapperCore/wrapperKraken/wrapperHumann/
        target:
          deployment: c3sfr1-slurm
          service: humann3
      - step: /wrapperCore/wrapperKraken/
        target:
          deployment: c3sfr1-slurm
          service: kraken
      - step: /wrapperCore/wrapperMetaphlan/wrapperHumann/
        target:
          deployment: c3sfr1-slurm
          service: humann3
      - step: /wrapperCore/wrapperMetaphlan/
        target:
          deployment: c3sfr1-slurm
          service: metaphlan4


database:
  type: sqlite
  config:
    connection: ./database/db

deployments:
  c3sfr1-ssh:
    type: ssh
    config:
      nodes:
        - c3sfr1.di.unito.it
      username: scontald
      sshKey: ~/.ssh/id_rsa
    workdir: /beegfs/home/scontald/streamflow_tmp/metagenome
  c3sfr1-slurm:
    type: slurm
    config:
      maxConcurrentJobs: 10
      services:
        kraken:
          file: ./sbatch/kraken2.sh
        genomemapper:
          file: ./sbatch/genomeMapper.sh
        metaphlan4:
          file: ./sbatch/metaphlan4.sh
        humann3:
          file: ./sbatch/humann3.sh
    wraps: c3sfr1-ssh