From 73d4b88e3a16a3c9c7a4d5ed9f89bb4e0da4524e Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Thu, 15 Apr 2021 18:01:28 +0200
Subject: [PATCH] [MODIF] update tpm folder #24
---
main.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/main.nf b/main.nf
index a633743..ce95d78 100644
--- a/main.nf
+++ b/main.nf
@@ -514,7 +514,7 @@ if (!params.dnase){
${bam1} ${bam2}
samtools sort -@ ${task.cpus} -m 800M \\
- -n -T ./tmp/ \\
+ -n \\
-o ${prefix}_bwt2merged.sorted.bam \\
${prefix}_bwt2merged.bam
@@ -635,7 +635,7 @@ if (!params.dnase){
prefix = pe_bam.toString() - ~/.bam/
"""
mapped_2hic_fragments.py -f ${frag_file} -r ${pe_bam} --all ${opts}
- sort -T ./tmp/ -k2,2V -k3,3n -k5,5V -k6,6n -o ${prefix}.validPairs ${prefix}.validPairs
+ sort -k2,2V -k3,3n -k5,5V -k6,6n -o ${prefix}.validPairs ${prefix}.validPairs
"""
}
}
@@ -663,7 +663,7 @@ else{
prefix = pe_bam.toString() - ~/.bam/
"""
mapped_2hic_dnase.py -r ${pe_bam} ${opts}
- sort -T ./tmp/ -k2,2V -k3,3n -k5,5V -k6,6n -o ${prefix}.validPairs ${prefix}.validPairs
+ sort -k2,2V -k3,3n -k5,5V -k6,6n -o ${prefix}.validPairs ${prefix}.validPairs
"""
}
}
@@ -690,7 +690,7 @@ process remove_duplicates {
mkdir -p stats/${sample}
## Sort valid pairs and remove read pairs with same starts (i.e duplicated read pairs)
- sort -T ./tmp/ -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \
+ sort -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \
awk -F"\\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=\$2 || c2!=\$5 || s1!=\$3 || s2!=\$6){print;c1=\$2;c2=\$5;s1=\$3;s2=\$6}' > ${sample}.allValidPairs
echo -n "valid_interaction\t" > stats/${sample}/${sample}_allValidPairs.mergestat
--
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