From 800931bff22fb4c466cf41ae0fe8ea60e2f5085f Mon Sep 17 00:00:00 2001
From: SPearce <simon.pearce@cruk.manchester.ac.uk>
Date: Thu, 1 Sep 2022 11:13:23 +0100
Subject: [PATCH] Add Sarek specific config

---
 conf/pipeline/sarek/crukmi.config | 33 +++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 conf/pipeline/sarek/crukmi.config

diff --git a/conf/pipeline/sarek/crukmi.config b/conf/pipeline/sarek/crukmi.config
new file mode 100644
index 0000000..0b2aecd
--- /dev/null
+++ b/conf/pipeline/sarek/crukmi.config
@@ -0,0 +1,33 @@
+// Profile config names for nf-core/configs
+
+params {
+  // Specific nf-core/configs params
+  config_profile_description = 'Cancer Research UK Manchester Institute HPC cluster profile provided by nf-core/configs'
+  config_profile_contact = 'Stephen Kitcatt, Simon Pearce (@skitcattCRUKMI, @sppearce)'
+  config_profile_url = 'http://scicom.picr.man.ac.uk/projects/user-support/wiki'
+}
+
+// Specific nf-core/sarek process configuration
+process {
+
+  withName: 'SAMTOOLS_MPILEUP' {
+    cpus   = 1
+    memory = { check_resource( 5.GB * task.attempt) }
+  }
+
+}
+
+def check_resource(obj) {
+    try {
+      if (obj.getClass() == nextflow.util.MemoryUnit && obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+        return params.max_memory as nextflow.util.MemoryUnit
+      else if (obj.getClass() == nextflow.util.Duration && obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+        return params.max_time as nextflow.util.Duration
+      else if (obj.getClass() == java.lang.Integer)
+        return Math.min(obj, params.max_cpus as int)
+      else
+        return obj
+    } catch (all) {
+        println "   ### ERROR ###   Max params max_memory:'${params.max_memory}', max_time:'${params.max_time}' or max_cpus:'${params.max_cpus}'  is not valid! Using default value: $obj"
+    }
+}