diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index d26d66807602c7565433e1c1dba47f3c7c73da18..2e9224244968c16be327bb0d7ceb92f50aa836e9 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
-"""
-}