From bf23c27b357b69afaf8dcad97d811e6e03d9c669 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Tue, 21 May 2024 14:11:40 +0200
Subject: [PATCH] add the pairtools command to output final pairs file
---
modules/local/hicstuff/build_matrix.nf | 3 +++
1 file changed, 3 insertions(+)
diff --git a/modules/local/hicstuff/build_matrix.nf b/modules/local/hicstuff/build_matrix.nf
index 0f9384d..7746449 100644
--- a/modules/local/hicstuff/build_matrix.nf
+++ b/modules/local/hicstuff/build_matrix.nf
@@ -11,6 +11,7 @@ process BUILD_MATRIX {
output:
tuple val(meta), path("${meta1.id}_*"), emit: matrix
path "*.log", emit: log_file
+ path "*.gz", emit: final_pairs
script:
@@ -21,6 +22,8 @@ process BUILD_MATRIX {
grep -v ^# ${idx_pairs} | sort -S 2G -k8,8n -k9,9n --parallel=1 >> ${args}.pre.pairs
hicstuff_build_matrix.py -p ${args}.pre.pairs -f ${fragments_list} -t graal -o ${args}
+ pairtools sort ${idx_pairs} --output ${idx_pairs}.gz --c1 chr1 --c2 chr2 --p1 pos1 --p2 pos2 --pt frag1
+
mv ${args} ${meta1.id}_${args}
mv hicstuff_matrix.log hicstuff_${meta1.id}_matrix_sparse.log
"""
--
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