From 9ec5b1768c2fdb0e1324100a473bf1fe5a051144 Mon Sep 17 00:00:00 2001
From: nfontrod <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:32:23 +0000
Subject: [PATCH] Rnaseq.nf : index_fasta and mapping_fasta
---
src/Rnaseq.nf | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/src/Rnaseq.nf b/src/Rnaseq.nf
index 0b9ec81..1b59e88 100644
--- a/src/Rnaseq.nf
+++ b/src/Rnaseq.nf
@@ -78,5 +78,45 @@ bedtools getfasta -name \
"""
}
+process index_fasta {
+ tag "$fasta.baseName"
+ publishDir "results/mapping/index/", mode: 'copy'
+
+ input:
+ file fasta from fasta_files_extracted
+
+ output:
+ file "*.index*" into index_files
+
+ script:
+"""
+kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
+> ${fasta.baseName}_kallisto_report.txt
+"""
+}
+
+
+process mapping_fastq {
+ tag "$reads"
+ cpus 4
+ publishDir "results/mapping/quantification/", mode: 'copy'
+
+ input:
+ file reads from fastq_files_trim
+ file index from index_files
+
+ output:
+ file "*" into counts_files
+
+ script:
+"""
+mkdir ${reads[0].baseName}
+kallisto quant -i ${index} -t ${task.cpus} \
+--bias --bootstrap-samples 100 -o ${reads[0].baseName} \
+${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
+"""
+}
+
+
--
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