From e6053196ddc74d8e8f4dfa4a9dedd84d13771339 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Thu, 13 May 2021 13:10:41 +0200
Subject: [PATCH] [BUG] fix binnify bug
---
main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/main.nf b/main.nf
index ecfce36..963c260 100644
--- a/main.nf
+++ b/main.nf
@@ -978,7 +978,7 @@ process compartment_calling {
script:
"""
- cooltools genome binnify ${chrsize} ${res} > genome_bins.txt
+ cooltools genome binnify --all-names ${chrsize} ${res} > genome_bins.txt
cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt
cooltools call-compartments --contact-type cis -o ${sample}_compartments ${cool}
awk -F"\t" 'NR>1{OFS="\t"; if(\$6==""){\$6=0}; print \$1,\$2,\$3,\$6}' ${sample}_compartments.cis.vecs.tsv | sort -k1,1 -k2,2n > ${sample}_compartments.cis.E1.bedgraph
--
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