some fixes for nf-core/eager to avoid offline

ktmeaton · Oct 2, 2020 · d06ade5 · d06ade5
1 parent 7ad09ed
commit d06ade5
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Showing 2 changed files with 12 additions and 12 deletions.
diff --git a/config/eager.config b/config/eager.config
@@ -231,21 +231,21 @@ params {
 process.container = 'nfcore/eager:dev'
 
 // Load base.config by default for all pipelines
-includeConfig 'conf/base.config'
+//includeConfig 'conf/base.config'
 
 // Load nf-core custom profiles from different Institutions
-try {
-  includeConfig "${params.custom_config_base}/nfcore_custom.config"
-} catch (Exception e) {
-  System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
+//try {
+//  includeConfig "${params.custom_config_base}/nfcore_custom.config"
+//} catch (Exception e) {
+//  System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
+//}
 
 // Load nf-core/eager custom profiles from different institutions
-try {
-  includeConfig "${params.custom_config_base}/pipeline/eager.config"
-} catch (Exception e) {
-  System.err.println("WARNING: Could not load nf-core/config/eager profiles: ${params.custom_config_base}/pipeline/eager.config")
-}
+//try {
+//  includeConfig "${params.custom_config_base}/pipeline/eager.config"
+//} catch (Exception e) {
+//  System.err.println("WARNING: Could not load nf-core/config/eager profiles: ${params.custom_config_base}/pipeline/eager.config")
+//}
 
 profiles {
   conda { process.conda = "$baseDir/environment.yml" }

diff --git a/profiles/graham/config.yaml b/profiles/graham/config.yaml
@@ -22,5 +22,5 @@ jobs : "10"
 # Where to put the .snakemake directory
 shadow-prefix: "/home/keaton/projects/def-briang/keaton/plague-phylogeography"
 # slurm execution
-cluster: "sbatch --parsable -t {resources.time_min} -A {resources.account} --cpus-per-task {resources.cpus} --mem-per-cpu={resources.mem_mb} -o workflow/logs_slurm/{rule}_%j.out -e workflow/logs_slurm/{rule}_%j.err --job-name {rule} --export=ALL,NXF_OPTS='-Xms50m -Xmx500m'"
+cluster: "sbatch --parsable -t {resources.time_min} -A {resources.account} --cpus-per-task {resources.cpus} --mem-per-cpu={resources.mem_mb} -o workflow/logs_slurm/{rule}_%j.out -e workflow/logs_slurm/{rule}_%j.err --job-name {rule} --export=ALL,NXF_OPTS='-Xms50m -Xmx{resources.mem_mb}m',NXF_OFFLINE='TRUE'"
 cluster-status: "workflow/scripts/slurm_status.py"