diff --git a/conf/pipeline/rnaseq/eddie.config b/conf/pipeline/rnaseq/eddie.config new file mode 100644 index 0000000..d8e76d0 --- /dev/null +++ b/conf/pipeline/rnaseq/eddie.config @@ -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=${(task.memory + 4.GB).bytes/task.cpus}"} +} + +} diff --git a/conf/pipeline/sarek/eddie.config b/conf/pipeline/sarek/eddie.config new file mode 100644 index 0000000..3e1b811 --- /dev/null +++ b/conf/pipeline/sarek/eddie.config @@ -0,0 +1,27 @@ +process { + + withName:MapReads { + cpus = 16 + } + withName:BuildDict { + cpus = 1 + clusterOptions = {"-l h_vmem=${(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=${(task.memory + 4.GB).bytes/task.cpus}"} + } +} diff --git a/pipeline/rnaseq.config b/pipeline/rnaseq.config new file mode 100644 index 0000000..1a27463 --- /dev/null +++ b/pipeline/rnaseq.config @@ -0,0 +1,13 @@ +/* + * ------------------------------------------------- + * nfcore/rnaseq custom profile Nextflow config file + * ------------------------------------------------- + * Config options for custom environments. + * Cluster-specific config options should be saved + * in the conf/pipeline/rnaseq folder and imported + * under a profile name here. + */ + +profiles { + eddie { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/eddie.config" } +} diff --git a/pipeline/sarek.config b/pipeline/sarek.config index 4ef48da..d781478 100644 --- a/pipeline/sarek.config +++ b/pipeline/sarek.config @@ -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" } } \ No newline at end of file