From bf96062e51603df43f4bfc22d1a417ac03d49332 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 7 Sep 2018 11:13:00 -0500
Subject: [PATCH] Revert and add outputs for genome param and ref to error exit
 output

---
 workflow/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflow/main.nf b/workflow/main.nf
index 96336fa..f3f3fca 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -8,7 +8,7 @@ params.fastq = "$baseDir/../test_data/*.fastq.gz"
 params.designFile = "$baseDir/../test_data/design.csv"
 params.genome = 'GRCh38'
 params.genomes = []
-params.ref = params.genome ? params.genomes[ ${params.genome} ].ref ?: false : false
+params.ref = params.genome ? params.genomes[ params.genome ].ref ?: false : false
 params.expectCells = 10000
 params.forceCells = 0
 
@@ -18,7 +18,7 @@ if( params.ref ){
     .fromPath(params.ref)
     .ifEmpty { exit 1, "referene not found: ${params.ref}" }
 } else {
-  exit 1, "No reference genome specified."
+  exit 1, "No reference genome specified. ${params.genome}  ${params.ref}"
 }
 
 // Define List of Files
-- 
GitLab