From 676669189675806000c0ef373394f28bdd5c6e90 Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Tue, 24 Jul 2018 13:23:49 +0200
Subject: [PATCH] Add Ban sorting from SAMtools
---
src/RNAseq_sen1D.nf | 51 +++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 51 insertions(+)
diff --git a/src/RNAseq_sen1D.nf b/src/RNAseq_sen1D.nf
index f9353bd..fd1858d 100644
--- a/src/RNAseq_sen1D.nf
+++ b/src/RNAseq_sen1D.nf
@@ -155,3 +155,54 @@ if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
fi
"""
}
+
+/* bams sorting */
+process sort_bam {
+ tag "$bam.baseName"
+ cpus 4
+
+ input:
+ file bam from bam_files
+
+ output:
+ file "*_sorted.bam" into sorted_bam_files
+
+ script:
+"""
+samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
+"""
+}
+
+/* bams indexing */
+
+process index_bam {
+ tag "$bam.baseName"
+ input:
+ file bam from sorted_bam_files
+ output:
+ file "*bam*" into indexed_bam_file
+ script:
+"""
+samtools index ${bam}
+"""
+}
+
+
+/* bams spliting */
+
+process split_bam {
+ tag "$bam.baseName"
+ cpus 2
+
+ input:
+ file bam from indexed_bam_files
+
+ output:
+ file "*_forward.bam*" into forward_bam_files
+ file "*_reverse.bam*" into reverse_bam_files
+ script:
+"""
+samtools view -hb -F 0x10 ${bam} > ${bam}_forward.bam &
+samtools view -hb -f 0x10 ${bam} > ${bam}_reverse.bam
+"""
+}
--
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