From 4ea6d96387d76c07aa2812a9cb22ee07a0b52943 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Thu, 20 Sep 2018 17:03:10 +0200
Subject: [PATCH] src/nf_modules/Hisat2/test/index.nf : test index creation
---
src/nf_modules/Hisat2/test/index.nf | 32 +++++++++++++++++++++++++++++
1 file changed, 32 insertions(+)
create mode 100644 src/nf_modules/Hisat2/test/index.nf
diff --git a/src/nf_modules/Hisat2/test/index.nf b/src/nf_modules/Hisat2/test/index.nf
new file mode 100644
index 00000000..7b30f7db
--- /dev/null
+++ b/src/nf_modules/Hisat2/test/index.nf
@@ -0,0 +1,32 @@
+/*
+* Hisat2 :
+* Imputs : fastq files
+* Imputs : fasta files
+* Output : bam files
+*/
+
+/* fasta indexing */
+params.fasta = "$baseDir/data/bam/*.fasta"
+
+log.info "fasta files : ${params.fasta}"
+
+Channel
+ .fromPath( params.fasta )
+ .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+ .set { fasta_file }
+
+process index_fasta {
+ tag "$fasta.baseName"
+ publishDir "results/mapping/index/", mode: 'copy'
+
+ input:
+ file fasta from fasta_file
+
+ output:
+ file "*.index*" into index_files
+
+ script:
+"""
+hisat2-build ${fasta} ${fasta.baseName}.index
+"""
+}
--
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