nextflow.config

manifest {
    mainScript = 'variant_calling.nf'
}

profiles {
    standard {
        executor = 'local'
        process.container = 'hadrieng/simple_variant_calling'
        docker.enabled = true
    }
    planet {
        executor = 'sge'

        process.$adapter_trimming.clusterOptions = '-S /bin/bash'
        process.$adapter_trimming.time = '30m'
        process.$adapter_trimming.cpus = 1
        process.$adapter_trimming.memory = '1G'
        process.$adapter_trimming.module = 'scythe'

        process.$quality_trimming.clusterOptions = '-S /bin/bash'
        process.$quality_trimming.time = '30m'
        process.$quality_trimming.cpus = 1
        process.$quality_trimming.memory = '1G'
        process.$quality_trimming.module = 'sickle'

        process.$bowtie.clusterOptions = '-S /bin/bash'
        process.$bowtie.penv = 'smp'
        process.$bowtie.time = '2h'
        process.$bowtie.cpus = 12
        process.$bowtie.memory = '1G'
        process.$bowtie.module = 'bowtie:SAMtools'

        process.$mpileup.clusterOptions = '-S /bin/bash'
        process.$mpileup.time = '30m'
        process.$mpileup.cpus = 1
        process.$mpileup.memory = '1G'
        process.$mpileup.module = 'SAMtools'
    }
}