From a49b62ab09017da3ddad4e874f47126acf7b0ecb Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Tue, 23 Jan 2024 09:50:35 +0100
Subject: [PATCH] correct sort for build matrix test full
---
bin/hicstuff_build_matrix.py | 3 ---
modules/local/hicstuff/build_matrix.nf | 4 +++-
2 files changed, 3 insertions(+), 4 deletions(-)
diff --git a/bin/hicstuff_build_matrix.py b/bin/hicstuff_build_matrix.py
index 8c47ac3..4ac69c1 100755
--- a/bin/hicstuff_build_matrix.py
+++ b/bin/hicstuff_build_matrix.py
@@ -71,9 +71,6 @@ def pairs2matrix(
# tmp_dir=tmp_dir,
# )
- cmd = 'grep -v ^# %s | sort -S 2G -k8,8n -k9,9n --parallel=1' % pairs_file
- with open(pre_mat_file, "w") as fout:
- fout.write(str(os.system(cmd)))
header_size = len(hio.get_pairs_header(pre_mat_file))
with open(pre_mat_file, "r") as pairs, open(mat_file, "w") as mat:
diff --git a/modules/local/hicstuff/build_matrix.nf b/modules/local/hicstuff/build_matrix.nf
index 4d531e9..f2db778 100644
--- a/modules/local/hicstuff/build_matrix.nf
+++ b/modules/local/hicstuff/build_matrix.nf
@@ -17,7 +17,9 @@ process BUILD_MATRIX {
def args = task.ext.args ?: ''
"""
- hicstuff_build_matrix.py -p ${idx_pairs} -f ${fragments_list} -t graal -o ${args}
+ grep -e ^# ${idx_pairs} > ${args}.pre.pairs
+ 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}
mv ${args} ${meta1.id}_${args}
"""
--
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