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nextflow.config
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nextflow.config
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manifest {
homePage = 'https://github.com/adigenova/nf-gene-fusions'
description = 'Gene fusion caller'
mainScript = 'main.nf'
author = 'Alex Di Genova'
version = '1.1'
name = 'gene-fusions'
}
// Load job.conf for process tagging
includeConfig 'conf/jobs.conf'
// Load genomes.config list the available genome reference
//todo: define the list of available here.
//includeConfig 'conf/genomes.conf'
profiles {
docker {
docker.enabled = true
process.container = 'iarcbioinfo/nf-gene-fusions:v1.1'
}
singularity {
singularity.enabled = true
process.container = 'iarcbioinfo/nf-gene-fusions:v1.1'
singularity.autoMounts = true
}
}
//additionals files for visualization of arriba results
params {
//default arriba lib location from the container
arriba_lib='/opt/conda/envs/gene-fusions/var/lib/arriba'
arriba_opt = false
arriba_plot = true
arriba_svs = false
// Options: Building STAR-star_index
star_index = false
fasta = false
gtf = false
read_length = 100
//Defaults for read data
reads = null
bams = null
reads_csv = null
svs = null
debug = false
help = false
// Shared default variables across different scripts
outdir = './results'
tracedir = "${params.outdir}/nf-pipeline_info"
ref_fa = null
ref_gtf = null
// Defaults
max_memory = 128.GB
max_cpus = 8
max_time = 240.h
//activate debug mode
debug = false
}
// Define timestamp, to avoid overwriting existing trace
def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
// nextflow run information
timeline {
enabled = true
file = "${params.tracedir}/${manifest.name}_${timestamp}_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/${manifest.name}_${timestamp}_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/${manifest.name}_${timestamp}_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/${manifest.name}_${timestamp}_dag.html"
}
//Mesage regarding errors or complete
workflow.onComplete = {
// any workflow property can be used here
println "Pipeline complete"
println "Command line: $workflow.commandLine"
}
workflow.onError = {
println "Oops... Pipeline execution stopped with the following message: ${workflow.errorMessage}"
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}