From b1f4bf87d47145fc92c9efdcaba8a45706b35bda Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 20 Jan 2021 17:25:28 +0100
Subject: [PATCH] nf_modules: add bedtools for DSL2
---
src/nf_modules/bedtools/main.nf | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
create mode 100644 src/nf_modules/bedtools/main.nf
diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
new file mode 100644
index 00000000..f4d67993
--- /dev/null
+++ b/src/nf_modules/bedtools/main.nf
@@ -0,0 +1,22 @@
+version = "2.25.0"
+container_url = "lbmc/bedtools:${version}"
+
+process fasta_from_bed {
+ container = "${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 getfasta -name \
+-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
+"""
+}
--
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