seqWell-ONT-plasmid-assembly/nextflow.config at main · seqwell/seqWell-ONT-plasmid-assembly · GitHub

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// ---- Global Docker settings ----
docker {
  enabled = true
  runOptions = '-u $(id -u):$(id -g)'
}

// ---- Global AWS credentials (only used if awsbatch profile is active) ----
aws {
  accessKey = '*'
  secretKey = '*'
  region = 'us-east-2'
}

// ---- Default parameters ----
params {
    input   = "test_data/fastq/"
    outdir  = "output"
    threads = 2
    jobs    = 2
}

// ---- Profiles ----
profiles {

  // --- For GitHub Actions CI or local dev ---
  test {
    process.executor = 'local'
    process.memory = '7 GB'
    process.cpus = 2
    docker.enabled = true
    params {
      input   = "test_data/fastq"
      outdir  = 'ci_output'
      threads = 2
      jobs    = 2

    }
  }

  // --- Optional: production run with AWS Batch ---
  awsbatch {

    aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'

    process {
      executor = 'awsbatch'
      queue = 'spot_low_priority'
      memory = '7 GB'
      cpus = 2

    withName:AUTOCYCLER {
        errorStrategy = { task.exitStatus in [143, 137, 104, 134, 139] ? 'retry' : 'finish' }
        maxRetries    = 1
        memory        = { 7.GB * task.attempt }
        container     = 'seqwell/autocycler:0.5.2'
    }


    withName:NANOSTAT {
        container = 'quay.io/biocontainers/nanostat:1.6.0--pyhdfd78af_0'
    }

     withName:PYSAMSTATS {
        container = 'quay.io/biocontainers/pysamstats:1.1.2--py311h384fd50_15'
    }

    withName:PLASMIDMAP {
        container = 'cautree/plasmidmap:latest'
    }

    withName:PLANNOTATE {
        container = 'seqwell/fq_assemble:v1.0'
    }
     withName:MINIMAP2 {
        container = 'cautree/minimap2'
    }

    withName:PLOT_COVERAGE {
        container = 'seqwell/python:v2.0'
    }

    }

    aws {
      accessKey = '*'
      secretKey = '*'
      region = 'us-east-2'
    }
  }
}

// ---- Process-specific settings (default local + docker) ----
process {
      executor = 'local'
      memory = '7 GB'
      cpus = 2

    withName:AUTOCYCLER {
        errorStrategy = { task.exitStatus in [143, 137, 104, 134, 139] ? 'retry' : 'finish' }
        maxRetries    = 1
        memory        = { 7.GB * task.attempt }
        container = 'seqwell/autocycler:0.5.2'
    }

    withName:NANOSTAT {
        container = 'quay.io/biocontainers/nanostat:1.6.0--pyhdfd78af_0'
    }

     withName:PYSAMSTATS {
        container = 'quay.io/biocontainers/pysamstats:1.1.2--py311h384fd50_15'
    }

    withName:PLASMIDMAP {
        container = 'cautree/plasmidmap:latest'
    }

    withName:PLANNOTATE {
        container = 'seqwell/fq_assemble:v1.0'
    }
     withName:MINIMAP2 {
        container = 'cautree/minimap2'
    }

    withName:PLOT_COVERAGE {
        container = 'seqwell/python:v2.0'
    }


}