From a744be62c5f56409ad6191ab3e7adbc30934f7f8 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Wed, 12 May 2021 19:55:36 +0200
Subject: [PATCH] [MODIF] add gc content for compartments
---
main.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/main.nf b/main.nf
index 8f6fffb..f7c977b 100644
--- a/main.nf
+++ b/main.nf
@@ -978,10 +978,10 @@ process compartment_calling {
script:
"""
- #cooltools genome binnify ${chrsize} ${res} > genome_bins.txt
- #cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt
+ cooltools genome binnify ${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
+ 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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