From 36c3cb4533227b6a127a4cad2a49f202b4588c4b Mon Sep 17 00:00:00 2001
From: gbenoit <gerard.benoit11@ens-lyon.fr>
Date: Wed, 6 Jun 2018 15:06:25 +0000
Subject: [PATCH] add Kallisto
---
src/RNAseq.nf | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index e73dc64..f1fb802 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -79,3 +79,43 @@ bedtools getfasta -name \
-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
"""
}
+
+process index_fasta {
+ tag "$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.toList()
+
+ 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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