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added pipeline-specific config

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This commit is contained in:
Mei Wu 2021-09-28 10:38:15 +02:00
parent 735100ed0b
commit 79a79f7d8d
3 changed files with 25 additions and 10 deletions
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9
conf/hasta.config
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@ -21,15 +21,6 @@ params {
process { process {
executor = 'slurm' executor = 'slurm'
clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" } clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" }
withName:'PICARD_MARKDUPLICATES' {
cpus = { check_max( 13 * task.attempt, 'cpus' ) }
memory = { check_max( 130.GB * task.attempt, 'memory' ) }
}
withName:'DEEPVARIANT' {
cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 80.GB * task.attempt, 'memory' ) }
}
} }
profiles { profiles {

11
conf/pipeline/raredisease/hasta.config Normal file
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@ -0,0 +1,11 @@
process {
withName:'PICARD_MARKDUPLICATES' {
cpus = { check_max( 13 * task.attempt, 'cpus' ) }
memory = { check_max( 130.GB * task.attempt, 'memory' ) }
}
withName:'DEEPVARIANT' {
cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 80.GB * task.attempt, 'memory' ) }
}
}

13
pipeline/raredisease.config Normal file
View file

@ -0,0 +1,13 @@
/*
* -------------------------------------------------
* nfcore/raredisease custom profile Nextflow config file
* -------------------------------------------------
* Config options for custom environments.
* Cluster-specific config options should be saved
* in the conf/pipeline/raredisease folder and imported
* under a profile name here.
*/
profiles {
hasta { includeConfig "${params.custom_config_base}/conf/pipeline/raredisease/hasta.config" }
}