diff --git a/Snakefile b/Snakefile
index e3908962e61d52ed3246d64fb76c5a4ee63ade43..fca50250c19a7a757691876c6385fd8d68ed77cd 100755
--- a/Snakefile
+++ b/Snakefile
@@ -71,9 +71,9 @@ else:
 sample_dir = config["input_dir"]
 analysis_dir = config["analysis_dir"]
 
-input_data = [sample_dir + "/{{SAMPLE}}{}.fastq.gz".format(rt1)]
+input_data = [sample_dir + "/{{SAMPLE}}{}{}".format(rt1,config["input_extension"])]
 if paired:
-    input_data += [sample_dir + "/{{SAMPLE}}{}.fastq.gz".format(rt2)]    
+    input_data += [sample_dir + "/{{SAMPLE}}{}{}".format(rt2,config["input_extension"])]    
 # global variable for all output files
 final_output = []
 
@@ -86,9 +86,9 @@ final_output = []
 #----------------------------------
 
 fastqc_input_fastq = input_data
-fastqc_output_done = "00-Fastqc/{SAMPLE}_R1_fastqc.fastq.gz"
+fastqc_output_done = "00-Fastqc/{{SAMPLE}}{}_fastqc{}".format(rt1,config["input_extension"])
 fastqc_wkdir = "00-Fastqc"
-fastqc_log = "00-Fastqc/logs/{SAMPLE}_R1_fastqc_raw.log"
+fastqc_log = "00-Fastqc/logs/{{SAMPLE}}{}_fastqc_raw.log".format(rt1)
 final_output.extend(expand(fastqc_output_done, SAMPLE=samples))
 include: os.path.join(RULES, "fastqc.rules")
 
@@ -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}_R1_trim.fastq.gz"]
+    adapters_output = ["01-Trimming/{{SAMPLE}}{}_trim{}".format(rt1,config["input_extension"])]
     if paired:
-        adapters_output += ["01-Trimming/{SAMPLE}_R2_trim.fastq.gz"]
+        adapters_output += ["01-Trimming/{{SAMPLE}}{}_trim{}".format(rt2,config["input_extension"])]
 
     # Set parameters
     adapters_options = config["adapters"]["options"]
diff --git a/config/cluster_config.json b/config/cluster_config.json
index 30defdfcf4dd9bf661e69d3c8513c7b41cc30d63..94e59c4587cca65b26d98ee56ec4ce2f8e9d308d 100644
--- a/config/cluster_config.json
+++ b/config/cluster_config.json
@@ -26,6 +26,15 @@
 	},
 
 	"bowtie2_index" :
+	{
+		"ram" : "60G"
+	},
+	"kallisto_quant" :
+	{
+		"ram" : "30G"
+	},
+
+	"kallisto_index" :
 	{
 		"ram" : "60G"
 	}