add rule for strainphlan

tools/strainphlan/sample2markers/README.md

@@ -2,6 +2,9 @@
 
 This step will reconstruct all species strains found in metaphlan output sam file and store them in a pickle file (*.pkl). Those strains are referred as sample-reconstructed strains.
 
+.. **Note**: output pkl file is written should be written in a individual directory since the script tries
+    to create and write into a `tmp` dir that leads to error when running sample2markers.py in parallel.
+
 ### Help section
 
 ```

tools/strainphlan/strainphlan/Snakefile

+__strainphlan_exec_command = config.get('strainphlan', {}).get('exec_command', 'strainphlan')
+__strainphlan_modules = config.get('strainphlan', {}).get('modules')
+__strainphlan_options = config.get('strainphlan', {}).get('options', "")
+__strainphlan_threads = config.get('strainphlan', {}).get('threads', 1)
+
+
+rule strainphlan:
+    input:
+        __strainphlan_input
+    output:
+        __strainphlan_output
+    params:
+        exec_command = __strainphlan_exec_command,
+        modules = __strainphlan_modules,
+        clade = __strainphlan_clade,
+        output_dir = __strainphlan_output_dir,
+        options = __strainphlan_options
+    threads:
+        __strainphlan_threads
+    run:
+        command = []
+        if params.modules:
+            command.append("module load {params.modules}")
+        command.append("{params.exec_command} -s {input} -n {threads} -c {params.clade} {params.options} -o {params.output_dir}")
+        shell(" && ".join(command))

tools/strainphlan/strainphlan/config.yaml

+input_dir: data
+
+strainphlan:
+  threads: 4
+  exec_command: sample2markers.py