fix output condition

maxulysse · maxulysse · commit c0a3ead998e8 · 2022-11-25T16:52:16.000+01:00
diff --git a/conf/modules/haplotypecaller.config b/conf/modules/haplotypecaller.config
@@ -119,7 +119,7 @@ process {
         ]
     }
 
-    if (!(params.tools && params.tools.split(',').contains('haplotypecaller'))) {
+    if (params.tools && params.tools.split(',').contains('haplotypecaller')) {
         withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)' {
             ext.prefix       = { "${meta.id}.realigned" }
             publishDir       = [

Original file line number	Diff line number	Diff line change
`@@ -119,7 +119,7 @@ process {`
`119`	`119`	`]`
`120`	`120`	`}`
`121`	`121`
`122`		`- if (!(params.tools && params.tools.split(',').contains('haplotypecaller'))) {`
	`122`	`+ if (params.tools && params.tools.split(',').contains('haplotypecaller')) {`
`123`	`123`	`withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM\|INDEX_MERGE_BAM)' {`
`124`	`124`	`ext.prefix = { "${meta.id}.realigned" }`
`125`	`125`	`publishDir = [`