From da8cf2f20705f4fca348c8a6185dada9430092b4 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Wed, 24 Mar 2021 10:46:26 +0000
Subject: [PATCH] Added pipeline-specific config files for rnaseq and sarek

---
 conf/pipeline/rnaseq/eddie.config | 15 +++++++++++++++
 conf/pipeline/sarek/eddie.config  | 27 +++++++++++++++++++++++++++
 pipeline/rnaseq.config            | 13 +++++++++++++
 pipeline/sarek.config             |  1 +
 4 files changed, 56 insertions(+)
 create mode 100644 conf/pipeline/rnaseq/eddie.config
 create mode 100644 conf/pipeline/sarek/eddie.config
 create mode 100644 pipeline/rnaseq.config

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