From 123e0076e4e228716f810b922c358c526e073aaf Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 17 Nov 2022 14:29:05 +0100
Subject: [PATCH] add example for fastq_screen
---
src/nf_modules/fastq_screen/main.nf | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
create mode 100644 src/nf_modules/fastq_screen/main.nf
diff --git a/src/nf_modules/fastq_screen/main.nf b/src/nf_modules/fastq_screen/main.nf
new file mode 100644
index 00000000..6dbc8ec0
--- /dev/null
+++ b/src/nf_modules/fastq_screen/main.nf
@@ -0,0 +1,29 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "0.11.3--pl5.22.0_0"
+container_url = "quay.io/biocontainers/fastq-screen:${version}"
+
+params.fastq_screen = ""
+params.fastq_screen_out = ""
+process fastq_screen {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+ if (params.index_fasta_out != "") {
+ publishDir "results/${params.fastq_screen_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(file_id), path(fastq)
+
+ output:
+ tuple val(file_id), path("*"), emit: output
+
+ script:
+"""
+fastq_screen --get_genomes
+fastq_screen --threads ${task.cpus} sample1.fastq sample2.fastq
+"""
+}
--
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