From 6fffaaeea2857f1f7c4e6e4c8f55a8841e93e160 Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Thu, 2 Jul 2020 10:48:12 +0200
Subject: [PATCH] add src/norm_coverage and add coverage calcul to RNAseq
worflow
---
src/RNAseq.nf | 22 +++++++++++++++++++++-
src/norm_coverage.sh | 34 ++++++++++++++++++++++++++++++++++
2 files changed, 55 insertions(+), 1 deletion(-)
create mode 100644 src/norm_coverage.sh
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 8515e966..791d4b0a 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -129,6 +129,7 @@ samtools index ${file_id}_sorted.bam
"""
}
+sorted_bam_files.into{sorted_bam_htseq, sorted_bam_coverage}
/* HTseq */
@@ -136,7 +137,7 @@ process sort_bam {
tag "$file_id"
input:
- set file_id, file(bam) from sorted_bam_files
+ set file_id, file(bam) from sorted_bam_htseq
output:
set file_id, "*_htseq.bam" into sorted_bam_files_2
@@ -188,3 +189,22 @@ htseq-count ${bam[0]} ${gtf} \
"""
}
+
+process coverage {
+ tag "$file_id"
+ publishDir "${params.output}/05_coverage/", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from sorted_bam_coverage
+
+ output:
+ file "*.bw" into coverage_files
+
+ script:
+"""
+bash src/norm_coverage.sh -b ${bam} \
+ -o {file_id}.bw \
+ --binSize 1 \
+ -p ${cpus} 8
+"""
+}
diff --git a/src/norm_coverage.sh b/src/norm_coverage.sh
new file mode 100644
index 00000000..8dcf4c83
--- /dev/null
+++ b/src/norm_coverage.sh
@@ -0,0 +1,34 @@
+#!/usr/bin/env bash
+
+set -e
+
+usage() { echo "Usage: $0 -b <bamfile.bam> -o <outputName> --binSize <int> -p <CPUs>" 1>&2; exit 1; }
+
+cpus=4
+binSize=1
+
+while getopts "b:o:binSize:p:" arg; do
+ case $arg in
+ -h)
+ echo "usage"
+ ;;
+ -b)
+ bam=$OPTARG
+ ;;
+ -o)
+ output=$OPTARG
+ ;;
+ --binSize)
+ binSize=$OPTARG
+ ;;
+ -p)
+ cpus=$OPTARG
+ ;;
+ esac
+done
+
+hg38=$(samtools view ${bam} | awk '{print $1}' | sort | uniq | wc -l)
+factor=$(echo "1000000/($hg38)" | bc -l)
+echo "hg38 counts : $hg38"
+echo "scaling factor : $factor\n"
+bamCoverage -p ${cpus} --scaleFactor ${factor} --binSize ${binSize} -b ${bam} -o ${output}
--
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