From 9f221f84cc66ca121a46d8f68db8f727dec523c9 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 12 Apr 2022 10:12:17 +0200
Subject: [PATCH] Only supply single input channel to profiling, as these are
 merged into single input channel at run_merging

---
 subworkflows/local/profiling.nf | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index c74c583..07b6b72 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -9,8 +9,7 @@ include { METAPHLAN3                  } from '../../modules/nf-core/modules/meta
 
 workflow PROFILING {
     take:
-    shortreads // [ [ meta ], [ reads ] ]
-    longreads // [ [ meta ], [ reads ] ]
+    reads // [ [ meta ], [ reads ] ]
     databases // [ [ meta ], path ]
 
     main:
@@ -22,9 +21,9 @@ workflow PROFILING {
     */
 
     // e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
-    ch_input_for_profiling = shortreads
-            .mix( longreads )
+    ch_input_for_profiling = reads
             .combine(databases)
+            .dump(tag: "combined_withdbs")
             .branch {
                 malt:    it[2]['tool'] == 'malt'
                 kraken2: it[2]['tool'] == 'kraken2'