nextflow.config

params {
    ref = "https://github.com/parklab/NGSCheckMate/raw/master/SNP/SNP.pt"
    outdir = false
    paired_fastq_samplesheet = false
    paired_fastq_path = false
    help = false

    cpus = 4
    memory_gb = 30

    container__ngscheckmate = "quay.io/biocontainers/ngscheckmate:1.0.0--py27r41hdfd78af_3"
    tracedir              = "${params.outdir}/pipeline_info"
}


profiles {
	kutral {
		singularity.enabled    = true
		singularity.autoMounts = true
		singularity.cacheDir   = 'work/singularity'
		singularity.runOptions = ' --bind /mnt/beegfs/labs/ '
		docker.enabled         = false
		podman.enabled         = false
		shifter.enabled        = false
		charliecloud.enabled   = false
		executor.name          = 'slurm'
		executor.queue         = 'uohhm'
		executor.queueSize     = 100
	}
}

process {
	errorStrategy = 'retry'
}

def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')

timeline {
	enabled = true
	file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
	enabled = true
	file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
	enabled = true
	file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
	enabled = true
	file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
}