increase genebody coverage mem

torres-alexis · torres-alexis · commit 4a6ef36e6c00 · 2025-03-27T09:58:15.000-07:00
diff --git a/RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/local.config b/RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/local.config
@@ -50,14 +50,13 @@ process {
         memory = { 16.GB * task.attempt }
     }
     withName:INFER_EXPERIMENT {
-        // To do: test 2, 1-2gb, consider qualimap alternatives for rseqc processes
         cpus   = { 2    * task.attempt }
         memory = { 2.GB * task.attempt }
     }
     withName:GENEBODY_COVERAGE {
-        // To do: test 2, 1-2gb
+        // To do: compare duration
         cpus   = { 2    * task.attempt }
-        memory = { 2.GB * task.attempt }
+        memory = { 4.GB * task.attempt }
     }
     withName:INNER_DISTANCE {
         // To do: test mem >2
diff --git a/RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/slurm.config b/RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/slurm.config
@@ -51,14 +51,13 @@ process {
         memory = { 16.GB * task.attempt }
     }
     withName:INFER_EXPERIMENT {
-        // To do: test 2, 1-2gb, consider qualimap alternatives for rseqc processes
         cpus   = { 2    * task.attempt }
         memory = { 2.GB * task.attempt }
     }
     withName:GENEBODY_COVERAGE {
-        // To do: test 2, 1-2gb
+        // To do: compare duration
         cpus   = { 2    * task.attempt }
-        memory = { 2.GB * task.attempt }
+        memory = { 4.GB * task.attempt }
     }
     withName:INNER_DISTANCE {
         // To do: test mem >2

Original file line number	Diff line number	Diff line change
`@@ -50,14 +50,13 @@ process {`
`50`	`50`	`memory = { 16.GB * task.attempt }`
`51`	`51`	`}`
`52`	`52`	`withName:INFER_EXPERIMENT {`
`53`		`- // To do: test 2, 1-2gb, consider qualimap alternatives for rseqc processes`
`54`	`53`	`cpus = { 2 * task.attempt }`
`55`	`54`	`memory = { 2.GB * task.attempt }`
`56`	`55`	`}`
`57`	`56`	`withName:GENEBODY_COVERAGE {`
`58`		`- // To do: test 2, 1-2gb`
	`57`	`+ // To do: compare duration`
`59`	`58`	`cpus = { 2 * task.attempt }`
`60`		`- memory = { 2.GB * task.attempt }`
	`59`	`+ memory = { 4.GB * task.attempt }`
`61`	`60`	`}`
`62`	`61`	`withName:INNER_DISTANCE {`
`63`	`62`	`// To do: test mem >2`
Original file line number	Diff line number	Diff line change
`@@ -51,14 +51,13 @@ process {`
`51`	`51`	`memory = { 16.GB * task.attempt }`
`52`	`52`	`}`
`53`	`53`	`withName:INFER_EXPERIMENT {`
`54`		`- // To do: test 2, 1-2gb, consider qualimap alternatives for rseqc processes`
`55`	`54`	`cpus = { 2 * task.attempt }`
`56`	`55`	`memory = { 2.GB * task.attempt }`
`57`	`56`	`}`
`58`	`57`	`withName:GENEBODY_COVERAGE {`
`59`		`- // To do: test 2, 1-2gb`
	`58`	`+ // To do: compare duration`
`60`	`59`	`cpus = { 2 * task.attempt }`
`61`		`- memory = { 2.GB * task.attempt }`
	`60`	`+ memory = { 4.GB * task.attempt }`
`62`	`61`	`}`
`63`	`62`	`withName:INNER_DISTANCE {`
`64`	`63`	`// To do: test mem >2`