From c114a62915735a05e4469c25bcf4829b0acee619 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 20 Sep 2020 11:21:07 -0500
Subject: [PATCH] Reduce species inference cutoffs
---
workflow/rna-seq.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index c7b9cb1..a940778 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -599,12 +599,12 @@ process inferMetadata {
echo -e "LOG: inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.log
# determine species
- if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 25)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 25)) ]
+ if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 40)) ]
then
species="Homo sapiens"
bam="GRCh.sampled.sorted.bam"
bed="./GRCh/bed/genome.bed"
- elif [ 1 -eq \$(echo \$(expr \${align_mo} ">=" 25)) ] && [ 1 -eq \$(echo \$(expr \${align_hu} "<" 25)) ]
+ elif [ 1 -eq \$(echo \$(expr \${align_mo} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_hu} "<" 40)) ]
then
species="Mus musculus"
bam="GRCm.sampled.sorted.bam"
--
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