Fix publishDir pattern for prokka outputs

BCCDC-PHL · May 15, 2024 · bf05f40 · bf05f40
1 parent 4353a05
commit bf05f40
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/modules/prokka.nf b/modules/prokka.nf
@@ -4,7 +4,7 @@ process prokka {
 
     errorStrategy 'ignore'
 
-    publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_prokka.{gbk,gff}", mode: 'copy'
+    publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_prokka.{gbk,gff}", mode: 'copy'
 
     input:
     tuple val(sample_id), path(assembly), val(assembler), val(assembly_mode)