nextflow.config

params {
    // Pipeline stuff
    fq = false
    db_uri = 'ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p+h+v.tar.gz'
    hg_uri = 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz'
    outdir = 'output'
   
    // Boilerplate
    name = false
    help = false
    tracedir = "${params.outdir}/pipeline_info"
    
}

profiles {
  conda { process.conda = "$baseDir/environment.yml" }
  docker { docker.enabled = true }
  singularity { singularity.enabled = true }
  slurm { process.executor = 'slurm' }
}

process.container = 'sbi6mjb/qc_nextflow'

timeline {
  enabled = true
  file = "${params.tracedir}/execution_timeline.html"
}
report {
  enabled = true
  file = "${params.tracedir}/execution_report.html"
}
trace {
  enabled = true
  file = "${params.tracedir}/execution_trace.txt"
}
dag {
  enabled = true
  file = "${params.tracedir}/pipeline_dag.svg"
}