From 4538e8aa36d71b06cbf46a68f82596f513b1c506 Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Thu, 7 Jul 2022 13:41:42 +0200
Subject: [PATCH] Update medair.config

- added path to singularity image for Sentieon
- harmonized alignment
---
 conf/medair.config | 36 +++++++++++++++++++++---------------
 1 file changed, 21 insertions(+), 15 deletions(-)

diff --git a/conf/medair.config b/conf/medair.config
index 183d4f6..eeda705 100644
--- a/conf/medair.config
+++ b/conf/medair.config
@@ -1,13 +1,13 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)'
-  config_profile_contact = 'Clinical Genomics, Gothenburg'
-  config_profile_url = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/'
+  config_profile_contact     = 'Clinical Genomics, Gothenburg'
+  config_profile_url         = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/'
 }
 
 //Nextflow parameters
 singularity {
-    enabled = true
+    enabled  = true
     cacheDir = "/apps/bio/dependencies/nf-core/singularities"
 }
 
@@ -15,26 +15,32 @@ profiles {
   
   wgs {
     process {
-      queue = 'wgs.q'
-      executor = 'sge'
-      penv = 'mpi'
+      queue                  = 'wgs.q'
+      executor               = 'sge'
+      penv                   = 'mpi'
       process.clusterOptions = '-l excl=1'
-      params.max_cpus = 40
-      params.max_time = 48.h
-      params.max_memory = 128.GB
+      params.max_cpus        = 40
+      params.max_time        = 48.h
+      params.max_memory      = 128.GB
     }
   }
 
   production {
     process {
-      queue = 'production.q'
-      executor = 'sge'
-      penv = 'mpi'
+      queue                  = 'production.q'
+      executor               = 'sge'
+      penv                   = 'mpi'
       process.clusterOptions = '-l excl=1'
-      params.max_cpus = 40
-      params.max_time = 480.h
-      params.max_memory = 128.GB
+      params.max_cpus        = 40
+      params.max_time        = 480.h
+      params.max_memory      = 128.GB
     }
   }
 }
 
+//Specific parameter for pipelines that can use Sentieon (e.g. nf-core/sarek, nf-core/raredisease)
+process {
+  withLabel:'sentieon' {
+    container = "/apps/bio/singularities/sentieon-211204-peta.simg"
+  }
+}