From 79a79f7d8dd8b7bdc91b30e295780bf41342b59a Mon Sep 17 00:00:00 2001
From: Mei Wu <savantmei@gmail.com>
Date: Tue, 28 Sep 2021 10:38:15 +0200
Subject: [PATCH] added pipeline-specific config

---
 conf/hasta.config                      | 11 +----------
 conf/pipeline/raredisease/hasta.config | 11 +++++++++++
 pipeline/raredisease.config            | 13 +++++++++++++
 3 files changed, 25 insertions(+), 10 deletions(-)
 create mode 100644 conf/pipeline/raredisease/hasta.config
 create mode 100644 pipeline/raredisease.config

diff --git a/conf/hasta.config b/conf/hasta.config
index 031cd70..c5dd5e4 100644
--- a/conf/hasta.config
+++ b/conf/hasta.config
@@ -20,16 +20,7 @@ params {
 
 process {
     executor = 'slurm'
-    clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" }
-
-    withName:'PICARD_MARKDUPLICATES' {
-        cpus   = { check_max( 13      * task.attempt, 'cpus' ) }
-        memory = { check_max( 130.GB  * task.attempt, 'memory' ) }
-    }
-    withName:'DEEPVARIANT' {
-        cpus   = { check_max( 16      * task.attempt, 'cpus' ) }
-        memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
-    }
+    clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" }    
 }
 
 profiles {
diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
new file mode 100644
index 0000000..2c6ed48
--- /dev/null
+++ b/conf/pipeline/raredisease/hasta.config
@@ -0,0 +1,11 @@
+process {
+    
+    withName:'PICARD_MARKDUPLICATES' {
+        cpus   = { check_max( 13      * task.attempt, 'cpus' ) }
+        memory = { check_max( 130.GB  * task.attempt, 'memory' ) }
+    }
+    withName:'DEEPVARIANT' {
+        cpus   = { check_max( 16      * task.attempt, 'cpus' ) }
+        memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
+    }
+}
\ No newline at end of file
diff --git a/pipeline/raredisease.config b/pipeline/raredisease.config
new file mode 100644
index 0000000..796a38b
--- /dev/null
+++ b/pipeline/raredisease.config
@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/raredisease custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/raredisease folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  hasta { includeConfig "${params.custom_config_base}/conf/pipeline/raredisease/hasta.config" }  
+}