From a37b535cba86db20d813a29a56e69b834ea0a25a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 2 May 2020 13:57:05 -0500
Subject: [PATCH] Fix featureCounts

---
 workflow/rna-seq.nf | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 3047f84..6c6b116 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -822,10 +822,12 @@ process countData {
     echo "LOG: running countData on the data" >> ${repRID}.countData.err
     if [ "${ends}" == "se" ]
     then
-      featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.countData -g 'gene_name' --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
+      featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
+      #featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.countData -g 'gene_name' --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
     elif [ "${ends}" == "pe" ]
     then
-      featureCounts -R SAM -p -G ./genmome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.countData -g 'gene_name' --primary --ignoreDup -B ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
+      featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -p -B -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
+      #featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.countData -g 'gene_name' --primary --ignoreDup -B ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
     fi
 
     #Calculate TPM from the resulting countData table
-- 
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