Merge pull request #355 from b97pla/uppmax_miarka_config

added requirements for uppmax cluster miarka

conf/pipeline/sarek/uppmax.config

@@ -26,3 +26,15 @@ if (hostname ==~ "r.*") {
 if (hostname ==~ "i.*") {
   params.single_cpu_mem = 15.GB
 }
+
+// Miarka-specific config
+if (hostname ==~ "m.*") {
+  params.single_cpu_mem = 7.GB
+
+  process {
+    withName:MapReads {
+      cpus = {params.max_cpus}
+      memory = {params.max_memory}
+    }
+  }
+}

conf/uppmax.config

@@ -36,6 +36,20 @@ def clusterOptionsCreator = { m ->
         return base
     }
 
+    // cluster is miarka
+    if (hostname.startsWith("m")) {
+        // job will fit on a regular node
+        if (m <= 357.GB) {
+            return base
+        }
+        // job requires at least a 2TB node
+        if (m <= 2000.GB) {
+            return base + " --mem 2TB "
+        }
+        // job requires the largest node
+        return base + " --mem 4TB "
+    }
+
     if (m <= 250.GB) {
         return base + " -p node -C mem256GB "
     }
@@ -77,6 +91,15 @@ if (hostname.startsWith("i")) {
   params.config_profile_description = 'UPPMAX (Irma) cluster profile provided by nf-core/configs.'
 }
 
+// Cluster: Miarka
+if (hostname.startsWith("m")) {
+  params.max_memory = 357.GB
+  // but what about the 96-core node?
+  params.max_cpus = 48
+  params.max_time = 480.h
+  params.config_profile_description = 'UPPMAX (Miarka) cluster profile provided by nf-core/configs.'
+}
+
 // Cluster: Rackham
 if (hostname.startsWith("r")) {
   params.max_cpus = 20

docs/pipeline/sarek/uppmax.md

@@ -15,4 +15,4 @@ Example: `nextflow run nf-core/sarek -profile uppmax`
 Specific configurations for uppmax clusters has been made for sarek.
 
 - Set paths to reference genomes
-- Set path to singularity containers for `irma`
+- Override resource requirements for MapReads on `miarka`

docs/uppmax.md

@@ -64,9 +64,9 @@ The UPPMAX nf-core configuration profile uses the `hostname` of the active envir
 - `bianca`
   - cpus available: 16 cpus
   - memory available: 109 GB
-- `irma`
+- `miarka`
-  - cpus available: 16 cpus
+  - cpus available: 48 cpus
-  - memory available: 250 GB
+  - memory available: 357 GB
 
 ## Development config