fix: Move --outReadsUnmapped Fastx to shared section for parabricks

pinin4fjords · claude · pinin4fjords · commit ea55c5f9aa4a · 2026-02-06T10:06:58.000Z
This conditional was inside the !isPbrun gate, so pbrun would never
get the flag even when save_unaligned or contaminant_screening is set.

Co-Authored-By: Claude Opus 4.6 &lt;noreply@anthropic.com&gt;
diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config
@@ -50,9 +50,10 @@ process {
                         : ['--quantTranscriptomeBan Singleend']
                 }
 
-                if (params.save_unaligned || params.contaminant_screening) {
-                    args += ['--outReadsUnmapped Fastx']
-                }
+            }
+
+            if (params.save_unaligned || params.contaminant_screening) {
+                args += ['--outReadsUnmapped Fastx']
             }
 
             // For prokaryotic data, use CDS features and disable spliced alignment

Original file line number	Diff line number	Diff line change
`@@ -50,9 +50,10 @@ process {`
`50`	`50`	`: ['--quantTranscriptomeBan Singleend']`
`51`	`51`	`}`
`52`	`52`
`53`		`- if (params.save_unaligned \|\| params.contaminant_screening) {`
`54`		`- args += ['--outReadsUnmapped Fastx']`
`55`		`- }`
	`53`	`+ }`
	`54`	`+`
	`55`	`+ if (params.save_unaligned \|\| params.contaminant_screening) {`
	`56`	`+ args += ['--outReadsUnmapped Fastx']`
`56`	`57`	`}`
`57`	`58`
`58`	`59`	`// For prokaryotic data, use CDS features and disable spliced alignment`