Merge pull request #42 from Juke34/jacusa2

eascarrunz · web-flow · commit 2b1c7bf56884 · 2025-06-24T14:27:43.000+02:00
do not use container options on singularity
diff --git a/config/softwares.config b/config/softwares.config
@@ -25,7 +25,7 @@ process {
     }
     withLabel: "jacusa2" {
         container = singularity.enabled ? "${params.sifPath}/jacusa2.sif" : "jacusa2"
-        containerOptions = '--ulimit nofile=1024:1024'    // Limit number of file descriptors to avoid out of memory errors
+        containerOptions = singularity.enabled ? "" : '--ulimit nofile=1024:1024'    // Limit number of file descriptors to avoid out of memory errors
     }
     withLabel: 'minimap2' {
         container = 'quay.io/biocontainers/minimap2:2.26--he4a0461_1'

Original file line number	Diff line number	Diff line change
`@@ -25,7 +25,7 @@ process {`
`25`	`25`	`}`
`26`	`26`	`withLabel: "jacusa2" {`
`27`	`27`	`container = singularity.enabled ? "${params.sifPath}/jacusa2.sif" : "jacusa2"`
`28`		`- containerOptions = '--ulimit nofile=1024:1024' // Limit number of file descriptors to avoid out of memory errors`
	`28`	`+ containerOptions = singularity.enabled ? "" : '--ulimit nofile=1024:1024' // Limit number of file descriptors to avoid out of memory errors`
`29`	`29`	`}`
`30`	`30`	`withLabel: 'minimap2' {`
`31`	`31`	`container = 'quay.io/biocontainers/minimap2:2.26--he4a0461_1'`