From 70c7d906aabc537fe7477d29966ad3fc948c27e1 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 25 Jan 2021 16:13:47 +0100
Subject: [PATCH] bedtools: add bam to fastq convertion
---
src/nf_modules/bedtools/main.nf | 40 +++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index f4d67993..70314d7c 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -20,3 +20,43 @@ bedtools getfasta -name \
-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
"""
}
+
+process bam_to_fastq_singleend {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "${bed.baseName}"
+ publishDir "results/fasta/", mode: 'copy'
+
+ input:
+ path fasta
+ path bed
+
+ output:
+ path "*_extracted.fasta", emit: fasta
+
+ script:
+"""
+bedtools bamtofastq
+-i ${bam} -fq ${bam.baseName}.fastq
+"""
+}
+
+process bam_to_fastq_paired_end {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "${bed.baseName}"
+ publishDir "results/fasta/", mode: 'copy'
+
+ input:
+ path fasta
+ path bed
+
+ output:
+ path "*_extracted.fasta", emit: fasta
+
+ script:
+"""
+bedtools bamtofastq
+-i ${bam} -fq ${bam.baseName}_R1.fastq -fq2 ${bam.baseName}_R2.fastq
+"""
+}
--
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