From a882b6cbaa8bc7542111be1a25a304bbfdc93c39 Mon Sep 17 00:00:00 2001
From: Adrian Larkeryd <adrian.larkeryd@icr.ac.uk>
Date: Wed, 4 Mar 2020 15:00:33 +0000
Subject: [PATCH] adding icr_davros config files generic and sarek

---
 conf/icr_davros.config                | 31 +++++++++++++++++++++++++++
 conf/pipeline/sarek/icr_davros.config |  8 +++++++
 2 files changed, 39 insertions(+)
 create mode 100644 conf/icr_davros.config
 create mode 100644 conf/pipeline/sarek/icr_davros.config

diff --git a/conf/icr_davros.config b/conf/icr_davros.config
new file mode 100644
index 0000000..73e72ed
--- /dev/null
+++ b/conf/icr_davros.config
@@ -0,0 +1,31 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow nf-core config file for ICR davros HPC
+ * -------------------------------------------------
+ * Defines LSF process executor and singularity
+ * settings.
+ * 
+ */
+
+singularity {
+  enabled = true
+  runOptions = "--bind /mnt:/mnt --bind /data:/data"
+}
+executor {
+  # This is set because of an issue with too many
+  # singularity containers launching at once, they
+  # cause an singularity error with exit code 255.
+  submitRateLimit = "2 sec"
+}
+process {
+  executor = "LSF"
+}
+params {
+  # LSF cluster set up with memory tied to cores,
+  # it can't be requested. Locked at 12G per core. 
+  cpus = 10
+  max_cpus = 20
+  max_memory = 12.GB
+  max_time = 168.h
+  igenomes_base = "/mnt/scratch/DDS/SDDS/BIOINFCO/SHARED/genomes/igenomes"
+}
\ No newline at end of file
diff --git a/conf/pipeline/sarek/icr_davros.config b/conf/pipeline/sarek/icr_davros.config
new file mode 100644
index 0000000..9c1ea6a
--- /dev/null
+++ b/conf/pipeline/sarek/icr_davros.config
@@ -0,0 +1,8 @@
+process {
+  errorStrategy = {task.exitStatus in [104,134,137,139,141,143,255] ? 'retry' : 'finish'}
+  maxRetries = 5
+  withName:MapReads {
+    memory = {check_resource(12.GB)}
+    time = {check_resource(48.h * task.attempt)}
+  }
+}
\ No newline at end of file