From 9a6cdfc21e0cc594425c401f06382f81dbf2563c Mon Sep 17 00:00:00 2001
From: b97pla <pontus.larsson@medsci.uu.se>
Date: Thu, 24 Mar 2022 14:25:43 +0100
Subject: [PATCH] removed process-specific requirements for sarek, request
 miarka high-mem node

---
 conf/pipeline/sarek/uppmax.config | 7 -------
 conf/uppmax.config                | 3 +--
 docs/pipeline/sarek/uppmax.md     | 1 -
 3 files changed, 1 insertion(+), 10 deletions(-)

diff --git a/conf/pipeline/sarek/uppmax.config b/conf/pipeline/sarek/uppmax.config
index 21802a0..b52c4ff 100644
--- a/conf/pipeline/sarek/uppmax.config
+++ b/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}
-    }
-  }
 }
diff --git a/conf/uppmax.config b/conf/uppmax.config
index b6d4959..3b2a699 100644
--- a/conf/uppmax.config
+++ b/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.'
diff --git a/docs/pipeline/sarek/uppmax.md b/docs/pipeline/sarek/uppmax.md
index 36504b8..a4d89c2 100644
--- a/docs/pipeline/sarek/uppmax.md
+++ b/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`