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nextflow.config
executable file
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nextflow.config
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/*
* ------------------------------------------------------------------
* Nextflow config file for the NME Lab Euler cluster pipelines
* ------------------------------------------------------------------
*/
process {
/* ========================================================================================
DEFAULT PARAMETERS
======================================================================================== */
executor = 'slurm'
scratch = 'true'
queue = 'normal.4h'
memory = 5.GB
cpus = 1
errorStrategy = { sleep(Math.pow(2, task.attempt) * 30 as long); return 'retry' }
maxRetries = 3
/* ========================================================================================
MODULE LABELS
======================================================================================== */
withLabel: bismark {
cpus = 12
memory = { 20.GB * task.attempt }
//queue = { task.attempt > 2 ? 'normal.120h' : task.attempt > 1 ? 'normal.24h' : 'normal.4h' }
time = { task.attempt > 2 ? 120.hour : task.attempt > 1 ? 24.hour : 4.hour }
}
withLabel: bowtie2 {
cpus = 8
memory = { 20.GB * task.attempt }
//queue = { task.attempt > 2 ? 'normal.120h' : task.attempt > 1 ? 'normal.24h' : 'normal.4h' }
time = { task.attempt > 2 ? 120.hour : task.attempt > 1 ? 24.hour : 4.hour }
}
withLabel: hisat2 {
cpus = 8
memory = { 20.GB * task.attempt }
//queue = { task.attempt > 2 ? 'normal.120h' : task.attempt > 1 ? 'normal.24h' : 'normal.4h' }
time = { task.attempt > 2 ? 120.hour : task.attempt > 1 ? 24.hour : 4.hour }
}
withLabel: bismarkDeduplication {
cpus = 1
memory = { 20.GB * task.attempt }
//queue = { task.attempt > 2 ? 'normal.120h' : task.attempt > 1 ? 'normal.24h' : 'normal.4h' }
time = { task.attempt > 2 ? 120.hour : task.attempt > 1 ? 24.hour : 4.hour }
}
withLabel: BismarkMethylationExtractor {
cpus = 4
memory = { 20.GB * task.attempt }
//queue = { task.attempt > 2 ? 'normal.120h' : task.attempt > 1 ? 'normal.24h' : 'normal.4h' }
time = { task.attempt > 2 ? 120.hour : task.attempt > 1 ? 24.hour : 4.hour }
}
withLabel: bismark2bedGraph {
memory = { 20.GB * task.attempt }
maxRetries = 5
}
withLabel: coverage2Cytosine {
memory = { 20.GB * task.attempt }
maxRetries = 5
}
withLabel: fastqScreen {
cpus = 8
memory = { 30.GB * task.attempt }
//queue = { task.attempt > 2 ? 'normal.120h' : task.attempt > 1 ? 'normal.24h' : 'normal.4h' }
time = { task.attempt > 2 ? 120.hour : task.attempt > 1 ? 24.hour : 4.hour }
}
withLabel: trimGalore {
cpus = 4
memory = { 10.GB * task.attempt }
//queue = { task.attempt > 2 ? 'normal.120h' : task.attempt > 1 ? 'normal.24h' : 'normal.4h' }
time = { task.attempt > 2 ? 120.hour : task.attempt > 1 ? 24.hour : 4.hour }
}
withLabel: multiQC {
cpus = 4
memory = { 20.GB * task.attempt }
}
withLabel: samtools {
memory = { 20.GB * task.attempt }
}
withLabel: picard {
memory = { 40.GB * task.attempt }
}
withLabel: featureCounts {
cpus = 6
memory = { 36.GB * task.attempt }
}
}
/* ========================================================================================
PIPELINE INFO
======================================================================================== */
timeline {
enabled = true
file = "pipeline_info/execution_timeline.html"
}
report {
enabled = true
file = "pipeline_info/execution_report.html"
}
trace {
enabled = true
file = "pipeline_info/execution_trace.txt"
}
notification {
enabled = false
to = "${USER}@ethz.ch"
}
//dag {
// enabled = true
// file = "pipeline_info/pipeline_dag.svg"
// }
//tower {
// accessToken = "${TOWER_ACCESS_TOKEN}"
// enabled = true
//}