Merge pull request #356 from b97pla/uppmax_miarka_config

removed process-specific requirements for sarek, request miarka high-…

conf/pipeline/sarek/uppmax.config

@@ -30,11 +30,4 @@ if (hostname ==~ "i.*") {
 // 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

@@ -47,7 +47,7 @@ def clusterOptionsCreator = { m ->
             return base + " --mem 2TB "
         }
         // job requires the largest node
-        return base + " --mem 4TB "
+        return base + " -C mem4TB "
     }
 
     if (m <= 250.GB) {
@@ -94,7 +94,6 @@ if (hostname.startsWith("i")) {
 // 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.'

docs/pipeline/sarek/uppmax.md

@@ -15,4 +15,3 @@ Example: `nextflow run nf-core/sarek -profile uppmax`
 Specific configurations for uppmax clusters has been made for sarek.
 
 - Set paths to reference genomes
-- Override resource requirements for MapReads on `miarka`