updated memory param to fix #41

k-florek · k-florek · commit b33ca29aa78b · 2021-02-24T15:41:04.000-06:00
diff --git a/staphb_toolkit/workflows/cutshaw/cutshaw.nf b/staphb_toolkit/workflows/cutshaw/cutshaw.nf
@@ -88,7 +88,7 @@ process spades {
 
   script:
   """
-  spades.py --memory ${task.memory} -1 ${reads[0]} -2 ${reads[1]} -o ./spades_out
+  spades.py --memory ${task.memory.toGiga()} -1 ${reads[0]} -2 ${reads[1]} -o ./spades_out
   mv ./spades_out/contigs.fasta ${name}_contigs.fasta
   """
 }

Original file line number	Diff line number	Diff line change
`@@ -88,7 +88,7 @@ process spades {`
`88`	`88`
`89`	`89`	`script:`
`90`	`90`	`"""`
`91`		`- spades.py --memory ${task.memory} -1 ${reads[0]} -2 ${reads[1]} -o ./spades_out`
	`91`	`+ spades.py --memory ${task.memory.toGiga()} -1 ${reads[0]} -2 ${reads[1]} -o ./spades_out`
`92`	`92`	`mv ./spades_out/contigs.fasta ${name}_contigs.fasta`
`93`	`93`	`"""`
`94`	`94`	`}`