From 1189b9250b70bb687592fce52bd25258d500de4e Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Thu, 20 Sep 2018 17:05:17 +0200
Subject: [PATCH] src/nf_modules/Hisat2/test/bam_converter.nf : converting sam
to bam
---
src/nf_modules/Hisat2/test/bam_converter.nf | 32 +++++++++++++++++++++
1 file changed, 32 insertions(+)
create mode 100644 src/nf_modules/Hisat2/test/bam_converter.nf
diff --git a/src/nf_modules/Hisat2/test/bam_converter.nf b/src/nf_modules/Hisat2/test/bam_converter.nf
new file mode 100644
index 00000000..f9627eb0
--- /dev/null
+++ b/src/nf_modules/Hisat2/test/bam_converter.nf
@@ -0,0 +1,32 @@
+/*
+* SAMtools :
+* Imputs : sam files
+* Output : bam files
+*/
+
+/* sam to bam */
+params.sam = "$baseDir/data/bam/*.sam"
+
+log.info "sam files : ${params.sam}"
+
+Channel
+ .fromPath( params.sam )
+ .ifEmpty { error "Cannot find any sam files matching: ${params.sam}" }
+ .set { sam_files }
+
+process bam_converter {
+ tag "$sam"
+ cpus 4
+ publishDir "results/mapping/bam/", mode: 'copy'
+
+ input:
+ file sam from sam_files
+
+ output:
+ file "*.bam" into bam_files
+
+ script:
+"""
+samtools view -@ ${task.cpus} -bS ${sam} > ${sam.baseName}.bam
+"""
+}
--
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