From f172f4565e9c5bcfc0410b63e34a91fb29166ecf Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 22 Jan 2021 14:41:51 +0100
Subject: [PATCH] nf_modules: fastqc add DSL2
---
src/nf_modules/fastqc/main.nf | 40 +++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
create mode 100644 src/nf_modules/fastqc/main.nf
diff --git a/src/nf_modules/fastqc/main.nf b/src/nf_modules/fastqc/main.nf
new file mode 100644
index 00000000..4baa1873
--- /dev/null
+++ b/src/nf_modules/fastqc/main.nf
@@ -0,0 +1,40 @@
+version = "0.11.5"
+container_url = "lbmc/fastqc:${version}"
+
+process fastqc_fastq_pairedend {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "$pair_id"
+ publishDir "results/fastq/fastqc/", mode: 'copy'
+
+ input:
+ tuple val(pair_id), path(reads)
+
+ output:
+ path "*.{zip,html}", emit: report
+
+ script:
+"""
+fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
+${reads[0]} ${reads[1]}
+"""
+}
+
+process fastqc_fastq_singleend {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "$file_id"
+ publishDir "results/fastq/fastqc/", mode: 'copy'
+
+ input:
+ tuple val(file_id), path(reads)
+
+ output:
+ path "*.{zip,html}", emit: report
+
+ script:
+"""
+fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
+"""
+}
+
--
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