From 754fad7c8e01e5fbfccc88324aad78691a686b0c Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Fri, 7 Aug 2020 09:32:03 +0100
Subject: [PATCH] Update output paths

---
 software/fastqc/test/main.nf | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/software/fastqc/test/main.nf b/software/fastqc/test/main.nf
index c90ad2cc..6405805a 100755
--- a/software/fastqc/test/main.nf
+++ b/software/fastqc/test/main.nf
@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-params.outdir = "results/"
+params.outdir = "output/"
 params.publish_dir_mode = "copy"
 params.conda = false
 
@@ -13,11 +13,11 @@ include { FASTQC } from '../main.nf'
  */
 workflow test_single_end {
 
-    def reads = []
-    reads = [ [ id:'test', single_end:true ],
+    def input = []
+    input = [ [ id:'test', single_end:true ],
               [ file('input/test_single_end.fastq.gz', checkIfExists: true) ] ]
 
-    FASTQC ( reads, [:] )
+    FASTQC ( input, [ publish_dir:'test_single_end' ] )
 }
 
 /*
@@ -25,11 +25,11 @@ workflow test_single_end {
  */
 workflow test_paired_end {
 
-    def reads = []
-    reads = [ [ id:'test', single_end:false ],
+    def input = []
+    input = [ [ id:'test', single_end:false ],
               [ file('input/test_R1.fastq.gz', checkIfExists: true), file('input/test_R2.fastq.gz', checkIfExists: true) ] ]
 
-    FASTQC ( reads, [:] )
+    FASTQC ( input, [ publish_dir:'test_paired_end' ] )
 }
 
 workflow {