Mercurial > repos > rliterman > csp2

changeset 15:0d775868ee62

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"planemo upload"
author rliterman
date Tue, 03 Dec 2024 12:23:38 -0500
parents 074a2dc26b69
children 0efc98f25fd5
files CSP2/nextflow.config CSP2/subworkflows/alignData/main.nf CSP2/subworkflows/fetchData/main.nf
diffstat 3 files changed, 15 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/CSP2/nextflow.config	Tue Dec 03 11:09:33 2024 -0500
+++ b/CSP2/nextflow.config	Tue Dec 03 12:23:38 2024 -0500
@@ -12,6 +12,17 @@
 // Import profile settings
 includeConfig "conf/profiles.config"
 
+// CPU/memory settings
+process {
+    withLabel: 'mummerMem' {
+        cpus = 1
+        memory = '4 GB'
+    }
+    withLabel: 'skesaMem' {
+        memory = '12 GB'
+    }
+}
+
 // Global default params
 params {
 
--- a/CSP2/subworkflows/alignData/main.nf	Tue Dec 03 11:09:33 2024 -0500
+++ b/CSP2/subworkflows/alignData/main.nf	Tue Dec 03 12:23:38 2024 -0500
@@ -66,8 +66,7 @@
 
 process runMUMmer{
 
-    cpus = 1
-    memory '4 GB'
+    label 'mummerMem'
 
     input:
     tuple val(query_name),val(query_fasta),val(ref_name),val(ref_fasta)
--- a/CSP2/subworkflows/fetchData/main.nf	Tue Dec 03 11:09:33 2024 -0500
+++ b/CSP2/subworkflows/fetchData/main.nf	Tue Dec 03 12:23:38 2024 -0500
@@ -493,8 +493,10 @@
     assembled_data = assembly_output.map{it->tuple(it[0],it[3])}
 }
 process skesaAssemble{
-    memory '12 GB' // Add readcount/memory check?
+    label 'skesaMem'
 
+    cpus = skesa_cpus
+    
     input:
     tuple val(sample_name),val(read_type),val(read_location)