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nextflow.config.example
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manifest {
name = "splice_sim"
author = "Niko Popitsch, Tobias Neumann"
version = "0.1"
description = "splice-aware RNA simulator"
}
timeline {
enabled = true
file = "logs/execution_timeline.html"
}
profiles {
// Local profile
standard {
process.executor = 'local'
process.memory = '8 GB'
process.cpus = 1
}
// Local profile with more memory (e.g., for STAR)
local_big {
process.executor = 'local'
process.memory = '62 GB'
process.cpus = 8
}
// Slurm profile for running on the CLIP/CBE cluster - SMALL configuration
cbe_small {
process {
container = 'tobneu/splice_sim:1.0.0'
executor = 'slurm'
memory='64 GB'
queue = { task.memory <= 120.GB ? 'c' : 'm' }
clusterOptions = { ( task.queue == 'g' ? '--gres gpu:1 ' : '' ) << ( (task.queue == 'c' & task.time <= 1.h) ? '--qos rapid' : ( task.time <= 8.h ? '--qos short': ( task.time <= 48.h ? '--qos medium' : '--qos long' ) ) ) }
cpus='8'
time='8.h'
scratch = false
withName: 'build_model' {
clusterOptions = '--qos=short'
memory='500 MB'
cpus=1
time='1.h'
queue='c'
}
withName: 'simulate_reads' {
clusterOptions = '--qos=short'
memory='1 GB'
cpus=2
time='1.h'
queue='c'
}
withName: 'map_star' {
clusterOptions = '--qos=short'
memory='40 GB'
cpus=2
time='1.h'
queue='c'
}
withName: 'map_hisat_3n' {
clusterOptions = '--qos=short'
memory='16 GB'
cpus=10
time='1.h'
queue='c'
}
withName: 'map_merangs' {
clusterOptions = '--qos=short'
memory='80 GB'
cpus=2
time='1.h'
queue='c'
}
withName: 'map_segemehl' {
clusterOptions = '--qos=short'
memory='80 GB'
cpus=12
time='8.h'
queue='c'
}
withName: 'postprocess_bams' {
clusterOptions = '--qos=short'
memory='100 MB'
cpus=1
time='1.h'
queue='c'
}
withName: 'evaluate_bams' {
clusterOptions = '--qos=short'
memory='1 GB'
cpus=2
time='1.h'
queue='c'
}
withName: 'extract_feature_metadata' {
clusterOptions = '--qos=short'
memory='1 GB'
cpus=1
time='1.h'
queue='c'
}
withName: 'preprocess_results' {
clusterOptions = '--qos=short'
memory='1 GB'
cpus=1
time='1.h'
queue='c'
}
withLabel: 'highmem' {
clusterOptions = '--qos=short'
memory='200 GB'
cpus=16
time='8.h'
queue='m'
}
withLabel: 'long' {
clusterOptions = '--qos=long'
memory='200 GB'
cpus=16
time='4.d'
queue='m'
}
withName: 'preprocess_results' {
container = 'tobneu/splice_sim_r:1.0.0'
}
beforeScript = 'hostname; module purge; ml list; export DISPLAY=""; export R_LIBS_USER=""; export R_LIBS=""; export PYTHONPATH=""; export PERL5LIB="";'
}
singularity {
enabled = true
cacheDir = '/resources/containers'
}
}
// Slurm profile for running on the CLIP/CBE cluster - BIG configuration
cbe_big {
process {
container = 'tobneu/splice_sim:1.0.0'
executor = 'slurm'
memory='64 GB'
queue = { task.memory <= 120.GB ? 'c' : 'm' }
clusterOptions = { ( task.queue == 'g' ? '--gres gpu:1 ' : '' ) << ( (task.queue == 'c' & task.time <= 1.h) ? '--qos rapid' : ( task.time <= 8.h ? '--qos short': ( task.time <= 48.h ? '--qos medium' : '--qos long' ) ) ) }
cpus='8'
time='8.h'
scratch = false
withName: 'build_model' {
clusterOptions = '--qos=short'
memory='5 GB'
cpus=4
time='1.h'
queue='c'
}
withName: 'simulate_reads' {
clusterOptions = '--qos=long'
memory='30 GB'
cpus=4
time='4.d'
queue='c'
}
withName: 'map_star' {
clusterOptions = '--qos=short'
memory='40 GB'
cpus=10
time='8.h'
queue='c'
}
withName: 'map_hisat_3n' {
clusterOptions = '--qos=medium'
memory='16 GB'
cpus=16
time='1.d'
queue='c'
}
withName: 'map_merangs' {
clusterOptions = '--qos=medium'
memory='80 GB'
cpus=4
time='2.d'
queue='c'
}
withName: 'map_segemehl' {
clusterOptions = '--qos=medium'
memory='80 GB'
cpus=4
time='2.d'
queue='c'
}
withName: 'postprocess_bams' {
clusterOptions = '--qos=short'
memory='4 GB'
cpus=2
time='4.h'
queue='c'
}
withName: 'evaluate_bams' {
clusterOptions = '--qos=long'
memory='20 GB'
cpus=2
time='6.d'
queue='c'
}
withName: 'extract_feature_metadata' {
clusterOptions = '--qos=short'
memory='8 GB'
cpus=1
time='2.h'
queue='c'
}
withName: 'preprocess_results' {
clusterOptions = '--qos=short'
memory='50 GB'
cpus=1
time='1.h'
queue='c'
}
withLabel: 'highmem' {
clusterOptions = '--qos=short'
memory='200 GB'
cpus=16
time='8.h'
queue='m'
}
withLabel: 'long' {
clusterOptions = '--qos=long'
memory='200 GB'
cpus=16
time='4.d'
queue='m'
}
withName: 'preprocess_results' {
container = 'tobneu/splice_sim_r:1.0.0'
}
beforeScript = 'hostname; module purge; ml list; export DISPLAY=""; export R_LIBS_USER=""; export R_LIBS=""; export PYTHONPATH=""; export PERL5LIB="";'
}
singularity {
enabled = true
cacheDir = '/resources/containers'
}
}
}
workflow.onComplete = {
println "Completed at : $workflow.complete"
println "Status : ${workflow.success?'OK':'failed'}"
println "Duration : ${workflow.duration}"
println "work dir : ${workflow.workDir}"
println "exit status : ${workflow.exitStatus}"
println "Error report : ${workflow.errorReport?:'-'}"
println "Command line : ${workflow.commandLine}"
}