From 195619a61f084fb5c5768a5073f8278d7ae8f82f Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Fri, 16 Apr 2021 12:47:32 +0200
Subject: [PATCH] remove gc in compartments
---
main.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/main.nf b/main.nf
index c035bb9..da16001 100644
--- a/main.nf
+++ b/main.nf
@@ -969,10 +969,10 @@ process compartment_calling {
script:
"""
- cooltools genome binnify ${chrsize} ${res} > genome_bins.txt
- cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt
- cooltools call-compartments --reference-track genome_gc.txt --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
+ #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
"""
}
--
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