From a977bc9075b54681ee1c2abc9da3393cd7595a41 Mon Sep 17 00:00:00 2001
From: ChristopherBarrington <christopher.barrington@crick.ac.uk>
Date: Tue, 17 Oct 2023 11:08:46 +0100
Subject: [PATCH] Update eigscis.nf

include `--phasing-track` option to provide faithful classification of A/B compartments
---
 modules/local/cooltools/eigscis.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/cooltools/eigscis.nf b/modules/local/cooltools/eigscis.nf
index 0393bb9..dfc2148 100644
--- a/modules/local/cooltools/eigscis.nf
+++ b/modules/local/cooltools/eigscis.nf
@@ -26,7 +26,7 @@ process COOLTOOLS_EIGSCIS {
     """
     cooltools genome binnify --all-names ${chrsize} ${resolution} > genome_bins.txt
     cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt
-    cooltools eigs-cis ${args} -o ${prefix}_compartments ${cool}
+    cooltools eigs-cis ${args} --phasing-track genome_gc.txt -o ${prefix}_compartments ${cool}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":