Update subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf

EladH1 · pinin4fjords · web-flow · commit e2a60fa38141 · 2026-06-29T14:17:33.000+02:00
Co-authored-by: Jonathan Manning &lt;jonathan.manning@seqera.io&gt;
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
@@ -401,7 +401,7 @@ def validateInputParameters() {
         }
         if (!(params.aligner in ['star_salmon', 'star_rsem', 'hisat2'])) {
             error("Contaminant screening with '--contaminant_screening_input unmapped' is only supported with '--aligner star_salmon', '--aligner star_rsem', or '--aligner hisat2'. Use '--contaminant_screening_input trim_only' or '--contaminant_screening_input trimmed' for other aligners.")
-        }
+            error("Contaminant screening with '--contaminant_screening_input unmapped' is only supported with '--aligner star_salmon', '--aligner star_rsem', or '--aligner hisat2'. Use '--contaminant_screening_input raw', '--contaminant_screening_input trim_only', or '--contaminant_screening_input trimmed' for other aligners.")
     }
 
     // Check that Sylph database and taxonomy is provided if using Sylph

Original file line number	Diff line number	Diff line change
`@@ -401,7 +401,7 @@ def validateInputParameters() {`
`401`	`401`	`}`
`402`	`402`	`if (!(params.aligner in ['star_salmon', 'star_rsem', 'hisat2'])) {`
`403`	`403`	`error("Contaminant screening with '--contaminant_screening_input unmapped' is only supported with '--aligner star_salmon', '--aligner star_rsem', or '--aligner hisat2'. Use '--contaminant_screening_input trim_only' or '--contaminant_screening_input trimmed' for other aligners.")`
`404`		`- }`
	`404`	`+ error("Contaminant screening with '--contaminant_screening_input unmapped' is only supported with '--aligner star_salmon', '--aligner star_rsem', or '--aligner hisat2'. Use '--contaminant_screening_input raw', '--contaminant_screening_input trim_only', or '--contaminant_screening_input trimmed' for other aligners.")`
`405`	`405`	`}`
`406`	`406`
`407`	`407`	`// Check that Sylph database and taxonomy is provided if using Sylph`