diff --git a/Dockerfile b/Dockerfile
index fda1d9a4..ba371954 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -346,7 +346,7 @@ ENV ACTIONS_RUNNER_DEBUG=${ACTIONS_RUNNER_DEBUG} \
     OUTPUT_FOLDER=${OUTPUT_FOLDER} \
     OUTPUT_FORMAT=${OUTPUT_FORMAT} \
     RUN_LOCAL=${RUN_LOCAL} \
-    SNAKEMAKE_CONFIG_FILE=${SNAKEMAKE_CONFIG_FILE} \
+    SNAKEMAKE_SNAKEFMT_CONFIG_FILE=${SNAKEMAKE_SNAKEFMT_CONFIG_FILE} \
     TEST_CASE_RUN=${TEST_CASE_RUN} \
     VALIDATE_ALL_CODEBASE=${VALIDATE_ALL_CODEBASE} \
     VALIDATE_ANSIBLE=${VALIDATE_ANSIBLE} \
diff --git a/README.md b/README.md
index 03a4e9a4..bdcedfc7 100644
--- a/README.md
+++ b/README.md
@@ -222,7 +222,7 @@ But if you wish to select or exclude specific linters, we give you full control
 | **PYTHON_FLAKE8_CONFIG_FILE**     | `.flake8`             | Filename for [flake8 configuration](https://flake8.pycqa.org/en/latest/user/configuration.html) (ex: `.flake8`, `tox.ini`)                                                       |
 | **PYTHON_BLACK_CONFIG_FILE**      | `.python-black`       | Filename for [black configuration](https://github.com/psf/black/blob/master/docs/compatible_configs.md) (ex: `.isort.cfg`, `pyproject.toml`)                                     |
 | **RUBY_CONFIG_FILE**              | `.ruby-lint.yml`      | Filename for [rubocop configuration](https://docs.rubocop.org/rubocop/configuration.html) (ex: `.ruby-lint.yml`, `.rubocop.yml`)                                                 |
-| **SNAKEMAKE_CONFIG_FILE**         | `.snakefmt.toml`      | Filename for [Snakemake configuration](https://github.com/snakemake/snakefmt#configuration) (ex: `pyproject.toml`, `.snakefmt.toml`)                                             |
+| **SNAKEMAKE_SNAKEFMT_CONFIG_FILE**| `.snakefmt.toml`      | Filename for [Snakemake configuration](https://github.com/snakemake/snakefmt#configuration) (ex: `pyproject.toml`, `.snakefmt.toml`)                                             |
 | **TYPESCRIPT_ES_CONFIG_FILE**     | `.eslintrc.yml`       | Filename for [eslint configuration](https://eslint.org/docs/user-guide/configuring#configuration-file-formats) (ex: `.eslintrc.yml`, `.eslintrc.json`)                           |
 | **VALIDATE_ALL_CODEBASE**         | `true`                | Will parse the entire repository and find all files to validate across all types. **NOTE:** When set to `false`, only **new** or **edited** files will be parsed for validation. |
 | **VALIDATE_ANSIBLE**              | `true`                | Flag to enable or disable the linting process of the Ansible language.                                                                                                           |
diff --git a/lib/linter.sh b/lib/linter.sh
index 17120387..8a3becf8 100755
--- a/lib/linter.sh
+++ b/lib/linter.sh
@@ -119,8 +119,8 @@ R_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${R_FILE_NAME}" # Path to the R lint r
 RUBY_FILE_NAME="${RUBY_CONFIG_FILE:-.ruby-lint.yml}"            # Name of the file
 RUBY_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${RUBY_FILE_NAME}" # Path to the ruby lint rules
 # Snakemake Vars
-SNAKEMAKE_FILE_NAME="${SNAKEMAKE_CONFIG_FILE:-.snakefmt.toml}"                     # Name of the file
-SNAKEMAKE_SNAKEFMT_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SNAKEMAKE_FILE_NAME}" # Path to the snakemake lint rules
+SNAKEMAKE_SNAKEFMT_FILE_NAME="${SNAKEMAKE_SNAKEFMT_CONFIG_FILE:-.snakefmt.toml}"                     # Name of the file
+SNAKEMAKE_SNAKEFMT_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SNAKEMAKE_SNAKEFMT_FILE_NAME}" # Path to the snakemake lint rules
 # SQL Vars
 SQL_FILE_NAME=".sql-config.json"                              # Name of the file
 SQL_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SQL_FILE_NAME}" # Path to the SQL lint rules
@@ -1310,6 +1310,10 @@ GetLinterRules "PYTHON_BLACK"
 GetLinterRules "R"
 # Get Ruby rules
 GetLinterRules "RUBY"
+# Get Snakemake lint rules
+GetLinterRules "SNAKEMAKE_LINT"
+# Get Snakemake snakefmt rules
+GetLinterRules "SNAKEMAKE_SNAKEFMT"
 # Get SQL rules
 GetLinterRules "SQL"
 # Get Terraform rules
@@ -1932,7 +1936,7 @@ if [ "${VALIDATE_SNAKEMAKE_LINT}" == "true" ]; then
   # Lint the files with snakefmt #
   ################################
   # LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILTER_REGEX_INCLUDE" "FILTER_REGEX_EXCLUDE" "FILE_ARRAY"
-  LintCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" "\(Snakefile|.*\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}"
+  LintCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" ".*\(Snakefile\|\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}"
 
 fi
 
@@ -1944,7 +1948,7 @@ if [ "${VALIDATE_SNAKEMAKE_SNAKEFMT}" == "true" ]; then
   # Lint the files with snakefmt #
   ################################
   # LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILTER_REGEX_INCLUDE" "FILTER_REGEX_EXCLUDE" "FILE_ARRAY"
-  LintCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --check --compact-diff" "\(Snakefile|.*\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}"
+  LintCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --check --compact-diff" ".*\(Snakefile\|\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}"
 fi
 
 ######################