added code to cater for memory for every task attempt

ayoraind · Apr 6, 2023 · 5ab9d21 · 5ab9d21
1 parent 137d55d
commit 5ab9d21
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,4 @@ work
 *.nextflow*
 Sample_files
 .default_output
+GRCh38.primary_assembly.genome.fa
diff --git a/modules/processes.nf b/modules/processes.nf
@@ -28,7 +28,7 @@ process MINIMAP2_INDEX {
 
 process MINIMAP2_SAM {
     tag "$meta"
-
+    memory { 4.GB * task.attempt }
     errorStrategy { task.attempt <= 5 ? "retry" : "finish" }
     maxRetries 5
 
@@ -44,7 +44,7 @@ process MINIMAP2_SAM {
 
     script:
     """
-    minimap2 -ax map-ont -t 12 $index $reads  > ${meta}.sam
+    minimap2 -ax map-ont -t $task.cpus $index $reads  > ${meta}.sam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":