From 31af5d3947f433a4824810e6bec2752ee928a73d Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Fri, 5 Apr 2019 22:06:59 +0200
Subject: [PATCH] update stats
---
bin/mapping_stat.sh | 16 ----------------
main.nf | 15 ++++++++++++---
2 files changed, 12 insertions(+), 19 deletions(-)
delete mode 100755 bin/mapping_stat.sh
diff --git a/bin/mapping_stat.sh b/bin/mapping_stat.sh
deleted file mode 100755
index 774eac0..0000000
--- a/bin/mapping_stat.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/bash
-
-bam1=$1
-bam2=$2
-merged=$3
-tag=$4
-
-tot_reads=$(samtools view -c ${merged})
-map_reads=$(samtools view -c -F 4 ${merged})
-gmap_reads=$(samtools view -c -F 4 ${bam1})
-lmap_reads=$(samtools view -c -F 4 ${bam2})
-
-echo -e "total_${tag}\t$tot_reads"
-echo -e "mapped_${tag}\t$map_reads"
-echo -e "global_${tag}\t$gmap_reads"
-echo -e "local_${tag}\t$lmap_reads"
diff --git a/main.nf b/main.nf
index 705eba2..8f7f61b 100644
--- a/main.nf
+++ b/main.nf
@@ -475,6 +475,8 @@ process merge_mapping_steps{
script:
sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2)/
+ tag = prefix.toString() =~/_R1|_val_1/ ? "R1" : "R2"
+
"""
samtools merge -@ ${task.cpus} \\
-f ${prefix}_bwt2merged.bam \\
@@ -486,9 +488,16 @@ process merge_mapping_steps{
${prefix}_bwt2merged.bam
mv ${prefix}_bwt2merged.sorted.bam ${prefix}_bwt2merged.bam
-
- if [[ "${prefix}" =~ _R1|_val_1 ]]; then mapping_stat.sh ${bam1} ${bam2} ${prefix}_bwt2merged.bam "R1" > ${prefix}.mapstat; fi
- if [[ "${prefix}" =~ _R2|_val_2 ]]; then mapping_stat.sh ${bam1} ${bam2} ${prefix}_bwt2merged.bam "R2" > ${prefix}.mapstat; fi
+
+ echo "## ${prefix}" > ${prefix}.mapstat
+ echo -n "total_${tag}\t" >> ${prefix}.mapstat
+ samtools view -c ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
+ echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
+ samtools view -c -F 4 ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
+ echo -n "global_${tag}\t" >> ${prefix}.mapstat
+ samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
+ echo -n "local_${tag}\t" >> ${prefix}.mapstat
+ samtools view -c -F 4 ${bam2} >> ${prefix}.mapstat
"""
}
--
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