diff --git a/tools/cd-hit/Snakefile b/tools/cd-hit/Snakefile
index b91b63d977572be40a2ed531b3f65917e19c2fcf..e023f862fd424c5387ad06b42b76b818bc011791 100644
--- a/tools/cd-hit/Snakefile
+++ b/tools/cd-hit/Snakefile
@@ -85,22 +85,25 @@ Options
    "CD-HIT: accelerated for clustering the next generation sequencing data", Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu & Weizhong Li. Bioinformatics, (2012) 28:3150-3152
 """
 
-__cd-hit_exec_command = config.get('cd-hit', {}).get('exec_command', 'cd-hit')
-__cd-hit_modules = config.get('cd-hit', {}).get('modules')
-__cd-hit_options = config.get('cd-hit', {}).get('options', '')
+__cd_hit_exec_command = config.get('cd_hit', {}).get('exec_command', 'cd_hit')
+__cd_hit_modules = config.get('cd_hit', {}).get('modules')
+__cd_hit_options = config.get('cd_hit', {}).get('options', '')
+__cd_hit_threads = config.get('cd_hit', {}).get('threads', 1)
 
-rule cd-hit:
+rule cd_hit:
     input:
-        __cd-hit_input
+        __cd_hit_input
     output:
-        __cd-hit_output
+        __cd_hit_output
     params:
-        exec_command = __cd-hit_exec_command,
-        modules = __cd-hit_modules,
-        options = __cd-hit_options
+        exec_command = __cd_hit_exec_command,
+        modules = __cd_hit_modules,
+        options = __cd_hit_options
+    threads:
+        __cd_hit_threads
     run:
         command = []
         if params.modules:
         	command.append("module load {params.modules}")
-        command.append("{params.exec_command} {params.options} -i {input} -o {output}")
+        command.append("{params.exec_command} {params.options} -i {input} -T {threads} -o {output}")
         shell(" && ".join(command))
diff --git a/tools/cd-hit/example_usage/Snakefile b/tools/cd-hit/example_usage/Snakefile
index 0b0cb898462c83aba5a13d85569a136c7a838381..ebd2bfb42f0215f500971cda43cc0624a6dfa3b7 100644
--- a/tools/cd-hit/example_usage/Snakefile
+++ b/tools/cd-hit/example_usage/Snakefile
@@ -1,7 +1,7 @@
 configfile: "config.yaml"
 
 # ==== Snakefile path ====
-__cd-hit_rules = config.get("snakefiles", {}).get("cd-hit")
+__cd-hit_rules = config.get("snakefiles", {}).get("cd_hit")
 
 __main_output_dir = config.get('output_dir', 'output')
 
diff --git a/tools/cd-hit/example_usage/config.yaml b/tools/cd-hit/example_usage/config.yaml
index db42ab7d9f5cf8dfb3c804ae09b20e0bf91c646d..2bc908f4a338af56d39bcbe1bb7d71b5d7a30cc1 100644
--- a/tools/cd-hit/example_usage/config.yaml
+++ b/tools/cd-hit/example_usage/config.yaml
@@ -1,5 +1,5 @@
 snakefiles:
-    prodigal: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/cd-hit/Snakefile
+    cd_hit: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/cd-hit/Snakefile
 
 input_dir: /some/input/directory
 output_dir: /some/output/directory
@@ -9,6 +9,7 @@ samples:
 - test_00001
 - test_00002
 
-prodigal:
+cd_hit:
   exec_command: cd-hit
   modules: blast+/2.10.0 cd-hit
+  threads: 16