From de331fa799c88b30530a6646b0b48ebefddd6ea3 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 25 Jan 2021 15:55:33 +0100
Subject: [PATCH] samtools: nf_module add mapped and unmapped filter
---
src/nf_modules/samtools/main.nf | 35 +++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index ea757d8b..cf0d2158 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -18,6 +18,41 @@ samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > ${file_id}_filtered.bam
"""
}
+process filter_bam_mapped {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(bam)
+ path bed
+
+ output:
+ tuple val(file_id), path("*_filtered.bam"), emit: bam
+ script:
+"""
+samtools view -@ ${task.cpus} -F 4 -hb ${bam} -L ${bed} > ${file_id}_mapped.bam
+"""
+}
+
+process filter_bam_unmapped {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(bam)
+ path bed
+
+ output:
+ tuple val(file_id), path("*_filtered.bam"), emit: bam
+ script:
+"""
+samtools view -@ ${task.cpus} -f 4 -hb ${bam} > ${file_id}_unmapped.bam
+"""
+}
+
+
process index_bam {
container = "${container_url}"
label "big_mem_mono_cpus"
--
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