From 2f4e9ea89b4bc45a1977fa459b7af96b9685222a Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Sat, 21 Oct 2023 09:57:40 +0200
Subject: [PATCH] Fix bug in adapter2 passing

---
 tests/wrappers/subworkflows/demultiplex/test.yml  | 2 +-
 wrappers/subworkflows/demultiplex/main.nf         | 2 +-
 wrappers/subworkflows/demultiplex/nextflow.config | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/wrappers/subworkflows/demultiplex/test.yml b/tests/wrappers/subworkflows/demultiplex/test.yml
index eb3293c1..e6dc2bf8 100644
--- a/tests/wrappers/subworkflows/demultiplex/test.yml
+++ b/tests/wrappers/subworkflows/demultiplex/test.yml
@@ -19,7 +19,7 @@
     - "wrappers/subworkflows/demultiplex"
 
 - name: "test_wrappers_demultiplex_multi_pe"
-  command: nextflow run ./wrappers/subworkflows/demultiplex/main.nf -c ./tests/config/nextflow.config ---samplesheet ./tests/data/samplesheets/rna-samplesheet.csv --fastqs ./tests/data/fastq_list/multi_pe_fastq.csv
+  command: nextflow run ./wrappers/subworkflows/demultiplex/main.nf -c ./tests/config/nextflow.config ---samplesheet ./tests/data/samplesheets/clip-samplesheet.csv --fastqs ./tests/data/fastq_list/multi_pe_fastq.csv
   tags:
     - "wrappers"
     - "wrappers/subworkflows"
diff --git a/wrappers/subworkflows/demultiplex/main.nf b/wrappers/subworkflows/demultiplex/main.nf
index d2b2b685..a7ccca9a 100644
--- a/wrappers/subworkflows/demultiplex/main.nf
+++ b/wrappers/subworkflows/demultiplex/main.nf
@@ -18,5 +18,5 @@ workflow  {
 
     // Execute
     DEMULTIPLEX ( ch_samplesheet, ch_fastqs )
-    DEMULTIPLEX.out.fastq | view
+    //DEMULTIPLEX.out.fastq | view
 }
diff --git a/wrappers/subworkflows/demultiplex/nextflow.config b/wrappers/subworkflows/demultiplex/nextflow.config
index 5f9cc07e..057ef2ab 100644
--- a/wrappers/subworkflows/demultiplex/nextflow.config
+++ b/wrappers/subworkflows/demultiplex/nextflow.config
@@ -17,7 +17,7 @@ process {
         ext.args   = [
             "-m5 ${params.fiveprimemismatches}",
             "-m3 ${params.threeprimemismatches}",
-            "-a2 ${params.adapter2}",
+            params.adapter2 ? "-a2 ${params.adapter2}" : '',
             "-q ${params.phredquality}",
             "-q5 ${params.phred_quality_5_prime}",
             "-mt ${params.min_trim}",