nextflow-draft/nextflow.config at main · MJBioInfo/nextflow-draft · GitHub

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/*
================================================================================

Here add Amazon AWS or cluster info

================================================================================
*/


docker.enabled = true
docker.runOptions = '-u $(id -u):$(id -g)'


manifest {
  description = 'Running Nextflow script on Aws cloud9'
  author = 'majeed jamakhani'
  nextflowVersion = '>=22.10.0'
}


profiles {
  standard {
    process.container = 'nfcore/rnaseq:latest'
  }

  docker {
    process.container = 'nfcore/rnaseq:latest'
    docker.runOptions='-u $(id -u):$(id -g)'
    docker.enabled = true
  }

}


process {

    withName:BEFOREQC {
        container = 'biocontainers/fastqc:v0.11.9_cv7'
    }


    withName:SICKLE  {

        container = 'biocontainers/sickle:v1.33git20150314.f3d6ae3-1-deb_cv1'
    }


    withName:AFTERQC {
        container = 'biocontainers/fastqc:v0.11.9_cv7'
    }


    withName:MULTIQC {
        container = 'ewels/multiqc:latest'
    }

    withName:BWAINDEX {
        container = 'biocontainers/bwa:v0.7.17_cv1'
    }


}