Attempt to fix docker permissions issue

marine-omics · Sep 13, 2024 · d8a277a · d8a277a
1 parent d719256
commit d8a277a
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/conf/setonix.config b/conf/setonix.config
@@ -7,7 +7,7 @@ process {
   queue = 'work'
   cpus = 1
   time = '1h'
-  memory = '1800MB'
+  memory = '4000MB'
 
 
 
@@ -34,6 +34,10 @@ process {
     memory          = 40.GB 
   }
 
+  withName: 'gatk_mark_duplicates'{
+    memory = 20.GB
+  }
+
 
 }
 

diff --git a/modules/gatk.nf b/modules/gatk.nf
@@ -190,6 +190,7 @@ process gatk_genomicsdb_import {
         --reader-threads ${task.cpus} \
         --batch-size 50 \
         --L $region
+    chmod a+rx *.db
     """
 
 }