From 9e6a91aff929ddd12170278565771571c18f0dda Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 15 Dec 2022 13:25:01 +0100
Subject: [PATCH] Distinguish  Kraken2 from Bracken

---
 conf/modules.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index f50b20c..60ebaa4 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -351,7 +351,7 @@ process {
 
     withName: KRAKEN2_KRAKEN2 {
         ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}-${meta.db_name}.bracken" : "${meta.id}-${meta.db_name}" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}/" },
             mode: params.publish_dir_mode,
@@ -361,7 +361,7 @@ process {
 
     withName: BRACKEN_BRACKEN {
         errorStrategy = 'ignore'
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.bracken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" }
         publishDir = [
             path: { "${params.outdir}/bracken/${meta.db_name}/" },
             mode: params.publish_dir_mode,