From 5bc80c3dad753a171447af906992731ab87b12a4 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 25 Jan 2021 14:10:28 +0100
Subject: [PATCH] nf_module: sratoolkit add DSL2
---
src/nf_modules/sratoolkit/main.nf | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
create mode 100644 src/nf_modules/sratoolkit/main.nf
diff --git a/src/nf_modules/sratoolkit/main.nf b/src/nf_modules/sratoolkit/main.nf
new file mode 100644
index 00000000..c17d456f
--- /dev/null
+++ b/src/nf_modules/sratoolkit/main.nf
@@ -0,0 +1,27 @@
+version = "2.8.2"
+container_url = "lbmc/sratoolkit:${version}"
+
+process index_fasta {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "$sra"
+
+ input:
+ val sra
+
+ output:
+ tuple val(sra), path("*.fastq"), emit: fastq
+
+ script:
+"""
+fastq-dump --split-files --gzip ${sra}
+if [ -f ${sra}_1.fastq ]
+then
+ mv ${sra}_1.fastq ${sra}_R1.fastq
+fi
+if [ -f ${sra}_2.fastq ]
+then
+ mv ${sra}_2.fastq ${sra}_R2.fastq
+fi
+"""
+}
--
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