From 4c68aa57d64cd4021ec6fe259a87bbbb80f868fe Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Tue, 21 Jan 2020 17:01:52 -0600
Subject: [PATCH] Updated references location to more universal location
---
workflow/rna-seq.nf | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 1aa409b..c850e5b 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -157,6 +157,7 @@ endsManual = Channel.create()
stranded = Channel.create()
spike = Channel.create()
species = Channel.create()
+reference = file ("/project/BICF/BICF_Core/s181706/github/gudmap/rna-seq/References/GRCh38.p12/hisat2")
metadata.splitCsv(sep: ',', header: false).separate(
rep,
endsMeta,
@@ -249,4 +250,4 @@ process alignReads {
samtools view -1 --threads `nproc` -o ${repRID}.bam ${repRID}.sam 1>${repRID}.align.out 2> ${repRID}.align.err;
samtools sort -@ `nproc` -O BAM ${repRID}.bam 1>${repRID}.align.out 2> ${repRID}.align.err;
"""
-}
\ No newline at end of file
+}
--
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