From 519f8d1a90ae601ff4014afe3df11837d9ce51f5 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Thu, 20 Sep 2018 17:03:45 +0200
Subject: [PATCH] src/nf_modules/Hisat2/test/mapping_single.nf : test
mapping-SE
---
src/nf_modules/Hisat2/test/mapping_single.nf | 36 ++++++++++++++++++++
1 file changed, 36 insertions(+)
create mode 100644 src/nf_modules/Hisat2/test/mapping_single.nf
diff --git a/src/nf_modules/Hisat2/test/mapping_single.nf b/src/nf_modules/Hisat2/test/mapping_single.nf
new file mode 100644
index 00000000..f6740b72
--- /dev/null
+++ b/src/nf_modules/Hisat2/test/mapping_single.nf
@@ -0,0 +1,36 @@
+/*
+* for single-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*.fastq"
+params.index = "$baseDir/data/index/*.index*"
+
+log.info "fastq files : ${params.fastq}"
+log.info "index files : ${params.index}"
+
+Channel
+ .fromPath( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+Channel
+ .fromPath( params.index )
+ .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+ .set { index_files }
+
+process mapping_fastq {
+ tag "$reads.baseName"
+ cpus 4
+ publishDir "results/mapping/", mode: 'copy'
+
+ input:
+ file reads from fastq_files
+ file index from index_files.toList()
+
+ output:
+ file "*" into count_files
+
+ script:
+"""
+hisat2 -x ${file(file(index[0]).baseName).baseName} -U ${reads} -S ${reads.baseName}.sam -p ${task.cpus}
+"""
+}
--
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