From 50da233f7775cd3fa1b2186e7abc7cc08d0da3e9 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Fri, 6 May 2022 13:36:24 +0200
Subject: [PATCH] [MODIF] remove sort from get_valid_interaction
---
modules/local/hicpro/get_valid_interaction.nf | 2 --
modules/local/hicpro/get_valid_interaction_dnase.nf | 2 --
modules/local/hicpro/trim_reads.nf | 2 +-
3 files changed, 1 insertion(+), 5 deletions(-)
diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf
index 4942eac..399a9ec 100644
--- a/modules/local/hicpro/get_valid_interaction.nf
+++ b/modules/local/hicpro/get_valid_interaction.nf
@@ -29,8 +29,6 @@ process GET_VALID_INTERACTION {
--all \\
${args}
- sort -k2,2V -k3,3n -k5,5V -k6,6n -o ${bam.baseName}.validPairs ${bam.baseName}.validPairs
-
cat <<-END_VERSIONS > versions.yml
"${task.process}":
python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
diff --git a/modules/local/hicpro/get_valid_interaction_dnase.nf b/modules/local/hicpro/get_valid_interaction_dnase.nf
index f34433b..dd5b061 100644
--- a/modules/local/hicpro/get_valid_interaction_dnase.nf
+++ b/modules/local/hicpro/get_valid_interaction_dnase.nf
@@ -22,8 +22,6 @@ process GET_VALID_INTERACTION_DNASE {
-r ${bam} \\
${args}
- sort -k2,2V -k3,3n -k5,5V -k6,6n -o ${bam.baseName}.validPairs ${bam.baseName}.validPairs
-
cat <<-END_VERSIONS > versions.yml
"${task.process}":
python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
diff --git a/modules/local/hicpro/trim_reads.nf b/modules/local/hicpro/trim_reads.nf
index b54811f..89109af 100644
--- a/modules/local/hicpro/trim_reads.nf
+++ b/modules/local/hicpro/trim_reads.nf
@@ -26,7 +26,7 @@ process TRIM_READS {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
- python: \$(echo \$(python --version 2>&1) | sed 's/^Python//; s/ .*\$//')
+ gzip: \$(echo \$(gzip --version 2>&1) | head -1 | cut -d" " -f2)
END_VERSIONS
"""
}
--
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