Make genomics2 more efficient

marine-omics · Oct 4, 2024 · 31ec82e · 31ec82e
1 parent 326762e
commit 31ec82e
Showing 1 changed file with 22 additions and 2 deletions.
diff --git a/conf/genomics.config b/conf/genomics.config
@@ -1,13 +1,33 @@
 params {
-        max_cpus=64
-        max_memory=600.GB
+        max_cpus=80
+        max_memory=1000.GB
         fb_chunksize=1000000        
 }
 
 process {
   scratch = true
   stageInMode = 'symlink'
   executor = 'local'
+
+  withName: 'gatk_haplotype_caller'{
+    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
+    memory = { check_max( 10.GB * task.attempt, 'memory' ) }
+  }
+
+  withName: 'gatk_genomicsdb_import' {
+    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
+  }
+
+  withName: 'gatk_genotypegvcfs' {
+    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+  }
+
+
+  withName: 'stat'{
+    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
+  }
+
+
 }
 
 singularity {