diff --git a/Snakefile b/Snakefile
index 7ed23ee..16fb764 100644
--- a/Snakefile
+++ b/Snakefile
@@ -293,7 +293,8 @@ rule call_narrow_peaks:
         name        = "{treatment}_vs_{control}",        #this option will give the output name, has to be similar to the output
         format      = str(config['macs2']['format']),
         genomesize  = str(config['macs2']['genomesize']),
-        qvalue      = str(config['macs2']['qvalue'])
+        qvalue      = str(config['macs2']['qvalue']),
+        outdir      = str(config['macs2']['outdir'])
     log:
         RESULT_DIR + "logs/macs2/{treatment}_vs_{control}_peaks.narrowPeak.log"
     benchmark:
@@ -302,7 +303,7 @@ rule call_narrow_peaks:
         "envs/macs2.yaml"
     shell:
         """
-        macs2 callpeak -t {input.treatment} -c {input.control} {params.format} {params.genomesize} --name {params.name} --nomodel --bdg -q {params.qvalue} --outdir results/bed/ &>{log}
+        macs2 callpeak -t {input.treatment} -c {input.control} {params.format} {params.genomesize} --name {params.name} --nomodel --bdg -q {params.qvalue} --outdir {params.outdir} &>{log}
         """
 
 rule call_broad_peaks:
@@ -317,7 +318,8 @@ rule call_broad_peaks:
         name        = "{treatment}_vs_{control}",
         format      = str(config['macs2']['format']),
         genomesize  = str(config['macs2']['genomesize']),
-        qvalue      = str(config['macs2']['qvalue'])
+        qvalue      = str(config['macs2']['qvalue']),
+        outdir      = str(config['macs2']['outdir'])
     log:
         RESULT_DIR + "logs/macs2/{treatment}_vs_{control}_peaks.broadPeak.log"
     benchmark:
@@ -326,5 +328,5 @@ rule call_broad_peaks:
         "envs/macs2.yaml"
     shell:
         """
-        macs2 callpeak -t {input.treatment} -c {input.control} {params.format} --broad --broad-cutoff 0.1 {params.genomesize} --name {params.name} --nomodel --bdg -q {params.qvalue} --outdir results/bed/ &>{log}
+        macs2 callpeak -t {input.treatment} -c {input.control} {params.format} --broad --broad-cutoff 0.1 {params.genomesize} --name {params.name} --nomodel --bdg -q {params.qvalue} --outdir {params.outdir} &>{log}
         """