diff --git a/RGBEPP.d b/RGBEPP.d
index 168d1a6..56d31d6 100644
--- a/RGBEPP.d
+++ b/RGBEPP.d
@@ -581,8 +581,8 @@ void main(string[] args) {
     string DirHome = std.file.getcwd();
     string DirRaw = buildPath(DirHome, "00_raw");
     string DirQcTrim = buildPath(DirHome, "01_fastp");
-    string DirMap = buildPath(DirHome, "02_bowtie2");
-    string DirAssembly = buildPath(DirHome, "03_spades");
+    string DirAssembly = buildPath(DirHome, "02_spades");
+    string DirMap = buildPath(DirHome, "03_bowtie2");
     string DirBam = buildPath(DirHome, "04_bam");
     string DirVcf = buildPath(DirHome, "05_vcf");
     string DirConsensus = buildPath(DirHome, "06_consen");
@@ -715,6 +715,16 @@ void main(string[] args) {
         PathMacse = getValueFromConfig(ARG_C, "macse");
 	PathDelstop = getValueFromConfig(ARG_C, "delstop");
         PathTrimal = getValueFromConfig(ARG_C, "trimal");
+        
+	DirRaw = getValueFromConfig(ARG_C, "raw_dir");
+        DirQcTrim = getValueFromConfig(ARG_C, "fastp_dir");
+        DirAssembly = getValueFromConfig(ARG_C, "spades_dir");
+        DirMap = getValueFromConfig(ARG_C, "bowtie2_dir");
+        DirBam = getValueFromConfig(ARG_C, "bam_dir");
+        DirVcf = getValueFromConfig(ARG_C, "vcf_dir");
+        DirConsensus = getValueFromConfig(ARG_C, "consen_dir");
+        DirAlign = getValueFromConfig(ARG_C, "macse_dir"); 
+        DirTrim = getValueFromConfig(ARG_C, "trimal_dir"); 
 
     }
 
diff --git a/config.example b/config.example
index 5003056..8e9bfb0 100644
--- a/config.example
+++ b/config.example
@@ -9,3 +9,12 @@ exonerate	=	/usr/bin/exonerate
 macse		=	/usr/share/java/macse.jar
 delstop		=	/usr/bin/delstop
 trimal		=	/usr/bin/trimal
+raw_dir		=	00_raw
+fastp_dir	=	01_fastp
+spades_dir	=	02_spades
+bowtie2_dir	=	03_bowtie2
+bam_dir		=	04_bam
+vcf_dir		=	05_vcf
+consen_dir	=	06_consen
+macse_dir	=	07_macse
+trimal_dir	=	08_trimal