nextflow.config

manifest {
    mainScript = 'lncRNA-Annotation.nf'
}

params { 
  output = "results/"
} 

process {
    container = 'cbcrg/lncrna_annotation@sha256:97c2af4ff4c9c65b81db48fadc87e501c1c81f9138ed8269cb6fcd3042714766'
    publishDir = [path: params.output, mode: 'copy', overwrite: 'true']
} 

profiles {
    crg {
        process {
          executor='crg'
          queue='cn-el7'
          memory='32G'
          cpus='4'
          time='24h'
          scratch = true
        }
        docker.enabled = true
        docker.fixOwnership = true
    }
    rth {
        process {
          executor='pbs'
          queue='default'
          memory='64G'
          time='24h'
          clusterOptions='-l nodes=1:ppn=12:alone'
        }
    }
  test {
    params.genome  = "$baseDir/tutorial/genome/genome_chr38.fa"
    params.annotation   ="$baseDir/tutorial/annotation/annotation_chr38.gtf"
    params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 \\" 
    docker.enabled = true
  }
}