fix issues

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))

tools/cd-hit/example_usage/Snakefile

 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')
 

tools/cd-hit/example_usage/config.yaml

 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