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Added pipeline-specific config files for rnaseq and sarek

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ameyner2 2021-03-24 10:46:26 +00:00
parent b48136a62e
commit da8cf2f207
4 changed files with 56 additions and 0 deletions
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15
conf/pipeline/rnaseq/eddie.config Normal file
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@ -0,0 +1,15 @@
process {
withName : "PICARD_MARKDUPLICATES" {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName : "QUALIMAP_RNASEQ" {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName : "FASTQC" {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
}

27
conf/pipeline/sarek/eddie.config Normal file
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process {
withName:MapReads {
cpus = 16
}
withName:BuildDict {
cpus = 1
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:BamQC {
cpus = 8
memory = 128.GB
clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
}
withName:MarkDuplicates {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:BaseRecalibrator {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:ApplyBQSR {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GatherBQSRReports {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
}

13
pipeline/rnaseq.config Normal file
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/*
* -------------------------------------------------
* nfcore/rnaseq custom profile Nextflow config file
* -------------------------------------------------
* Config options for custom environments.
* Cluster-specific config options should be saved
* in the conf/pipeline/rnaseq folder and imported
* under a profile name here.
*/
profiles {
eddie { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/eddie.config" }
}

1
pipeline/sarek.config
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@ -12,4 +12,5 @@ profiles {
munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/uppmax.config" }
icr_davros { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/icr_davros.config" }
eddie { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/eddie.config" }
}