From 88dc32c08f0bff9158be878ca47a6df4aa9b668b Mon Sep 17 00:00:00 2001
From: elabaron <emmanuel.labaronne@ens-lyon.fr>
Date: Wed, 4 Nov 2020 13:36:36 +0100
Subject: [PATCH] RibosomeProfiling.nf : fix typo beug in coverage process
---
src/RibosomeProfiling.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/RibosomeProfiling.nf b/src/RibosomeProfiling.nf
index 82a96198..0f002d48 100644
--- a/src/RibosomeProfiling.nf
+++ b/src/RibosomeProfiling.nf
@@ -589,7 +589,7 @@ process coverage {
params.do_postgenome==false
shell:
'''
- genome=$(samtools view !{bam[0]} | awk '{print $1} | sort | uniq | wc -l)
+ genome=$(samtools view !{bam[0]} | awk '{print $1}' | sort | uniq | wc -l)
factor=$(awk -v c=$genome 'BEGIN {print 1000000/c}')
bamCoverage -p !{task.cpus} --binSize 1 -b !{bam[0]} -o !{file_id}.bigwig
'''
--
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