nextflow.config

workDir = "./work"
scratch = "./"
time='48h'

// plugins {
//   id 'nf-co2footprint@0.4.0'    
// }

process {

    withName: FETCH_RUN {
        conda = "$projectDir/conda/fastq_dl.yml"
        maxForks = 10
    }
    withName: FASTQ_DL {
        conda = "$projectDir/conda/fastq_dl.yml"
        maxForks = 15
    }
    withName: FASTERQ_DUMP {
        time='48h'
        conda = "$projectDir/conda/fastq_dl.yml"
    }
    withName: FASTQC {
        time='48h'
        conda = "$projectDir/conda/fastqc.yml"        
    }

    withName: FIND_ADAPTERS {
        conda = "$projectDir/conda/adapters.yml"
    }

    withName: FASTP {
        time='48h'
        conda = "$projectDir/conda/fastp.yml"
    }
    withName: COLLAPSE_FASTQ {
        time='48h'
        conda = "$projectDir/conda/base.yml"
    	maxForks = 5
    }
}

plugins {
  id 'nf-boost'
}

boost {
  cleanup = true
}


// conda.enabled = true

// define different profiles
profiles {
    singularity {
        enabled = true
        cacheDir = './singularity'
        process.container = "$projectDir/singularity/pipeline"
    }
    docker {
        docker.enabled = true
        process.container = 'pipeline-image:latest'
    }
    conda {
        enabled = true
    }

    standard {
   	    includeConfig 'config/standard.config'
    }
    hpc_slurm {
        includeConfig 'config/slurm.config'
    } 
    lsf {
        includeConfig 'config/lsf.config'
    }
}