From 09a3123f484f4fae4c616ad6ace3da61b01e4a0b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 30 Jul 2021 11:41:00 -0500
Subject: [PATCH] If ends force then override fastq read error

---
 rna-seq.nf | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/rna-seq.nf b/rna-seq.nf
index 3094d28..12b71dd 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -149,7 +149,7 @@ process getBag {
   input:
     path credential, stageAs: "credential.json" from deriva_getBag
     path replicateExportConfig
-
+f
   output:
     path ("*.zip") into bag
 
@@ -439,6 +439,11 @@ process parseMetadata {
         fastqReadError_details="**Number of reads do not match for R1 and R2:** there may be a trunkation or mismatch of fastq files"
       fi
     fi
+    if [ "${params.endsForce}" != "" ]
+    then
+      fastqReadError=false
+      fastqReadError_details=""
+    fi
 
     # save design file
     echo "\${endsMeta},\${endsRaw},\${endsManual},\${stranded},\${spike},\${species},\${readLength},\${exp},\${study}" > design.csv
-- 
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