From 97103dc2bc36e8b82f975499e5c1d6e2b9a01730 Mon Sep 17 00:00:00 2001
From: alapendr <audrey.lapendry@ens-lyon.fr>
Date: Wed, 6 Jun 2018 15:12:32 +0000
Subject: [PATCH] Rnaseq.nf : update

---
 src/RNAseq.nf | 32 +++-----------------------------
 1 file changed, 3 insertions(+), 29 deletions(-)

diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index d26d668..2e92242 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -128,7 +128,7 @@ process index_fasta {
   publishDir "results/mapping/index/", mode: 'copy'
 
   input:
-    file fasta from fasta_files
+    file fasta from fasta_files_extracted
 
   output:
     file "*.index*" into index_files
@@ -152,8 +152,8 @@ process mapping_fastq {
   publishDir "results/mapping/quantification/", mode: 'copy'
 
   input:
-  file reads from fastq_files
-  file index from index_files.toList()
+  file reads from fastq_files_trim
+  file index from index_files
 
   output:
   file "*" into counts_files
@@ -168,31 +168,5 @@ ${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
 }
 
 
-/*
-* for single-end data
-*/
-
-
-process mapping_fastq {
-  tag "$reads.baseName"
-  cpus 4
-  publishDir "results/mapping/quantification/", mode: 'copy'
-
-  input:
-  file reads from fastq_files_trim
-  file index from index_files
-
-  output:
-  file "*" into count_files
-
-  script:
-"""
-mkdir ${reads.baseName}
-kallisto quant -i ${index} -t ${task.cpus} --single
---bias --bootstrap-samples 100 -o ${reads.baseName} \
--l ${params.mean} -s ${params.sd} -o ./ \
-${reads} > ${reads.baseName}_kallisto_report.txt
-"""
-}
 
 
-- 
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