From 94c41f304b735ec3457e01df28d2bce20c230e72 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 22 Jan 2021 15:13:12 +0100
Subject: [PATCH] nf_modules: add sambamba to DSL2
---
src/nf_modules/sambamba/main.nf | 55 +++++++++++++++++++++++++++++++++
1 file changed, 55 insertions(+)
create mode 100644 src/nf_modules/sambamba/main.nf
diff --git a/src/nf_modules/sambamba/main.nf b/src/nf_modules/sambamba/main.nf
new file mode 100644
index 00000000..22614426
--- /dev/null
+++ b/src/nf_modules/sambamba/main.nf
@@ -0,0 +1,55 @@
+version = "0.6.7"
+container_url = "lbmc/sambamba:${version}"
+
+process index_bam {
+ container = "${container_url}"
+ label "big_mem__cpus"
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(bam)
+
+ output:
+ tuple val(file_id), path("*.bam*"), emit: bam
+
+ script:
+"""
+sambamba index -t ${task.cpus} ${bam}
+"""
+}
+
+process sort_bam {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(bam)
+
+ output:
+ tuple val(file_id), path("*.bam*"), emit: bam
+
+ script:
+"""
+sambamba sort -t ${task.cpus} -o ${file_id}_sorted.bam ${bam}
+"""
+}
+
+
+process split_bam {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(bam)
+
+ output:
+ tuple val(file_id), path("*_forward.bam*"), emit: bam_forward
+ tuple val(file_id), path("*_reverse.bam*"), emit: bam_reverse
+ script:
+"""
+sambamba view -t ${task.cpus} -h -F "strand == '+'" ${bam} > ${file_id}_forward.bam
+sambamba view -t ${task.cpus} -h -F "strand == '-'" ${bam} > ${file_id}_reverse.bam
+"""
+}
--
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