diff --git a/Snakefile b/Snakefile
index a7ada175b6610d3af34024cdc0762491b70aa9aa..1b22f8d2109cc0d40fe16e4eef0890d9adbd9135 100755
--- a/Snakefile
+++ b/Snakefile
@@ -100,9 +100,9 @@ if config["adapters"]["remove"] :
     adapter_tool = config["adapters"]["tool"]
     adapters_input_fastq = input_data
     adapters_wkdir = "01-Trimming"
-    adapters_output = ["01-Trimming/{{SAMPLE}}{}_trim{}".format(rt1,config["input_extension"])]
+    adapters_output = ["01-Trimming/{{SAMPLE}}{}_trim.fastq".format(rt1)]
     if paired:
-        adapters_output += ["01-Trimming/{{SAMPLE}}{}_trim{}".format(rt2,config["input_extension"])]
+        adapters_output += ["01-Trimming/{{SAMPLE}}{}_trim.fastq".format(rt2)]
 
     # Set parameters
     adapters_options = config["adapters"]["options"]
@@ -131,8 +131,8 @@ else:
 if config["genome"]["rRNA_mapping"] :
     sortmerna_input = adapters_output
     sortmerna_fasta = config["genome"]["ribo_fasta_file"]
-    sortmerna_outfile_rRNA = "02-Mapping/Ribo/{SAMPLE}_rRNA.fastq.gz"
-    sortmerna_outfile_no_rRNA = "02-Mapping/Ribo/{SAMPLE}_norRNA.fastq.gz"
+    sortmerna_outfile_rRNA = "02-Mapping/Ribo/{SAMPLE}_rRNA.fastq"
+    sortmerna_outfile_no_rRNA = "02-Mapping/Ribo/{SAMPLE}_norRNA.fastq"
     sortmerna_logs_err = "02-Mapping/Ribo/logs/{SAMPLE}_mapping.err"
     sortmerna_logs_out = "02-Mapping/Ribo/logs/{SAMPLE}_mapping.out"
     final_output.extend(expand(sortmerna_outfile_no_rRNA, SAMPLE=samples))