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nexflow.config
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nexflow.config
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params {
csv = null
debug = false
outdir = "/mnt/beegfs/home/efeliu/work2024/080524_nextflow_BRCA/Runs_nextflow_BRCA/rename_no_dedup"
//we make links for bwa index
//we declare bwa variables
aligner="bwa-mem2"
alt_js="bwa-postalt.js"
alt=false
hla=true
ref="NO_FILE"
//we declare elprep variables
dbsnp="NO_FILE"
dbindel="NO_FILE"
elpre_ref="NO_FILE"
/*
//we declare annovar variables
*/
}
/*
process {
withName: 'PRINT_VERSIONS()'{
cpus = 1
memory = '1 GB'
}
withName: 'FASTQC' {
cpus = 2
memory = '15 GB'
}
withName: 'BWAMEM' {
cpus = 4
memory = '8 GB'
}
withName: 'MERGEB' {
cpus = 4
memory = '10 GB'
}
withName: 'ELPREP' {
cpus = 4
memory = '4 GB'
}
withName: 'QUALIMAP' {
cpus = 4
memory = '4 GB'
}
withName: 'B2C' {
cpus = 4
memory = '4 GB'
}
withName: 'STRELKA_ONESAMPLE'{
cpus = 1
memory = '4 GB'
}
withName: 'STRELKA_POOL'{
cpus = 2
memory = '4 GB'
}
withName: 'ANNOVAR'{
cpus = 2
memory = '4 GB'
}
withName: 'DEEPVARIANT_ONESAMPLE' {
cpus = 8
memory = '40 GB'
}
withName: 'GLNEXUS_DEEPVARIANT' {
cpus = 4
memory = '10 GB'
}
withName: 'B2V' {
cpus = 4
memory = '10 GB'
}
}
*/
container {
enabled = true
}
profiles {
kutral {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
process.executor = 'slurm'
process.queue = 'uohhm'
}
uoh {
process {
executor = "slurm"
queue = 'uohhm'
}
}
conda {
process.conda = '$baseDir/conda.yml'
}
}
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
defaultBranch = 'main'
homePage = 'https://github.com/digenoma-lab/BRCA'
author = 'Manuel Muñoz'
version = '0.1'
}