From e52bb115ee18bffbb9f03147ae92e530c91c8113 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 1 May 2020 23:52:54 -0500
Subject: [PATCH] Fix SE alignSampleSummary output name

---
 workflow/rna-seq.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 917f199..211ff06 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -406,7 +406,7 @@ process alignSampleData {
     if [ "${ends}" == "se" ]
     then
       echo "LOG: running Hisat2 with single-end settings" >> ${repRID}.${ref}.alignSampleData.err
-      hisat2 -p `nproc` --add-chrname -S ${ref}.sampled.sam -x hisat2/genome -U ${fastq1} --summary-file ${repRID}.alignSampleSummary.txt --new-summary 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err
+      hisat2 -p `nproc` --add-chrname -S ${ref}.sampled.sam -x hisat2/genome -U ${fastq1} --summary-file ${ref}.alignSampleSummary.txt --new-summary 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err
     elif [ "${ends}" == "pe" ]
     then
       echo "LOG: running Hisat2 with paired-end settings" >> ${repRID}.${ref}.alignSampleData.err
-- 
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