Added pipeline-specific config files for rnaseq and sarek

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}"}
+}
+
+}

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}"}
+  }
+}

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" }
+}

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" }
 }