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`