diff --git a/Dockerfile b/Dockerfile
index 562b388..6d99cde 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,8 @@
 # We need .NET Core image for running parser
 FROM mcr.microsoft.com/dotnet/core/sdk:2.1
 
+ENV container=true
+
 # Expose port for process monitor
 EXPOSE 26002/tcp
 EXPOSE 26002/udp
@@ -15,11 +17,10 @@ COPY fuzzer /usr/local/fuzzer/fuzzer
 COPY parser /usr/local/fuzzer/parser
 COPY reporter /usr/local/fuzzer/reporter
 
-# And finally, copy the run script
-COPY run.sh /usr/local/bin/
-
 # Set working directory
 WORKDIR /usr/local/fuzzer/
 
+COPY run.sh /usr/local/fuzzer/run.sh
+
 # Set run script as an entry point of the container
-ENTRYPOINT ["run.sh"]
+ENTRYPOINT ["/usr/local/fuzzer/run.sh"]
diff --git a/README.md b/README.md
index 330cd5f..8bb34c2 100644
--- a/README.md
+++ b/README.md
@@ -65,7 +65,7 @@ Execute `run.sh config_file_path openapi_doc_file_path [custom_payloads_file_pat
 ### Docker
 You just need to run the container with following arguments:
 
-`docker run -p {host_port}:{container_port} -v $(pwd):/usr/local/fuzzer/mnt/ starek4/wfuzz:latest mnt/config.json mnt/sqta.yaml [mnt/custom_payloads.txt]`
+`docker run -p {host_port}:{container_port} -v $(pwd):/usr/local/fuzzer/mnt/ starek4/wfuzz:latest config.json sqta.yaml [custom_payloads.txt]`
 
 where files `config.json`, `sqta.yaml` and `custom_payloads` needs to be stored in the working directory.
 With parameter `-p` you also need to bind port number, which is used for communication with your web API, to the container.
diff --git a/run.sh b/run.sh
index fbbd599..ed1b91a 100644
--- a/run.sh
+++ b/run.sh
@@ -9,25 +9,11 @@ then
     exit 1
 fi
 
-# Check if config file and documentation file are valid files
+# Load script arguments
 WFUZZ_CONFIG=$1
 OPENAPI_DOCUMENTATION=$2
 CUSTOM_PAYLOADS_FILE=$3
 
-if [ ! -f "$WFUZZ_CONFIG" ]
-then
-    echo "Configuration file path is not valid!" >&2
-    echo $USAGE >&2
-    exit 1
-fi
-
-if [ ! -f "$OPENAPI_DOCUMENTATION" ]
-then
-    echo "OpenApi documentation file path is not valid!" >&2
-    echo $USAGE >&2
-    exit 1
-fi
-
 # Define binary binaries paths
 PIP3_BIN=pip3
 PYTHON3_BIN=python3
@@ -47,14 +33,33 @@ FUZZER_LOG=fuzzing.log
 XUNIT2HTML_XSL=./reporter/xunit_to_html.xsl
 SAXON9HE=./reporter/saxon9he.jar
 
-# If there is mounted Docker directory, write output files into it
-if [ -d "mnt/" ]; then
+# If we are in Docker container, write output files into mounted folder and append this folder before input files paths
+if [ "$container" = "true" ]; then
     echo "Founded mounted Docker directory, you can find WFuzz artifacts in your working directory."
+    WFUZZ_CONFIG="./mnt/$WFUZZ_CONFIG"
+    OPENAPI_DOCUMENTATION="./mnt/$OPENAPI_DOCUMENTATION"
+    CUSTOM_PAYLOADS_FILE="./mnt/$CUSTOM_PAYLOADS_FILE"
+
     FUZZER_LOG="./mnt/$FUZZER_LOG"
     JUNIT_TEST_REPORT="./mnt/$JUNIT_TEST_REPORT_FILENAME"
     HTML_TEST_REPORT="./mnt/$HTML_TEST_REPORT_FILENAME"
 fi
 
+# Check if config file and documentation file are valid files
+if [ ! -f "$WFUZZ_CONFIG" ]
+then
+    echo "Configuration file path is not valid!" >&2
+    echo $USAGE >&2
+    exit 1
+fi
+
+if [ ! -f "$OPENAPI_DOCUMENTATION" ]
+then
+    echo "OpenApi documentation file path is not valid!" >&2
+    echo $USAGE >&2
+    exit 1
+fi
+
 # Define docker images tags
 REPORTER_IMAGE_TAG=wfuzz:reporter