You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
59 lines
1.9 KiB
Plaintext
59 lines
1.9 KiB
Plaintext
/*
|
|
* -------------------------------------------------
|
|
* Nextflow config file for running nf-core eager on whole genome data
|
|
* -------------------------------------------------
|
|
* nextflow run nf-core/eager -profile maestro,<qos>,maestronuclear (where <qos> is long or normal)
|
|
*/
|
|
|
|
params {
|
|
|
|
config_profile_name = 'nf-core/eager nucleaer - human profile'
|
|
|
|
config_profile_description = "A simple profile for human nuclear genomes"
|
|
|
|
email = 'pluisi@pasteur.fr'
|
|
}
|
|
|
|
|
|
process {
|
|
errorStrategy = 'retry'
|
|
maxRetries = 2
|
|
|
|
withName:'makeBWAIndex'{
|
|
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
time = { check_max( 12.h * task.attempt, 'time' ) }
|
|
}
|
|
withName:'adapter_removal'{
|
|
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
|
|
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
|
time = { check_max( 12.h * task.attempt, 'time' ) }
|
|
}
|
|
withName:'bwa'{
|
|
cpus = { check_max( 15 * task.attempt, 'cpus' ) }
|
|
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
|
time = 24.h
|
|
}
|
|
withName:'markduplicates'{
|
|
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
|
|
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
time = { check_max( 6.h * task.attempt, 'time' ) }
|
|
}
|
|
withName:'damageprofiler'{
|
|
cpus = 1
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
time = { check_max( 6.h * task.attempt, 'time' ) }
|
|
}
|
|
withName:'fastp'{
|
|
cpus = 8
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
time = { check_max( 6.h * task.attempt, 'time' ) }
|
|
}
|
|
withName:'fastqc'{
|
|
cpus = 2
|
|
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
|
|
time = { check_max( 6.h * task.attempt, 'time' ) }
|
|
}
|
|
}
|