From 84d25149e88bc33481c8ace0723826a3eaecb9e5 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 25 Jun 2018 16:40:30 -0500
Subject: [PATCH] Fix paired end.
---
workflow/main.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 3d2c720..fecc341 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -127,7 +127,7 @@ process alignReads {
if (pairedEnd) {
"""
- python3 $baseDir/scripts/map_reads.py -f $reads -r ${index}/genome.fa -p
+ python3 $baseDir/scripts/map_reads.py -f ${reads[0]} ${reads[1]} -r ${index}/genome.fa -p
"""
}
else {
@@ -250,7 +250,7 @@ process tssEnrich {
script:
"""
- sregistry pull bicf/metaseq:0.1.0
+ sregistry pull bicf/metaseq:0.1.0
singularity run $HOME/.singularity/shub/bicf-metaseq:0.1.0.simg $baseDir/scripts/atac_qc.py -b $deduped -p $sampleId -t $tssFile -c $chromSizes
"""
--
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