add example of workflow for metaphlan2

tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules

-__metaphlan2_heatmap_exec_command = config['metaphlan2_heatmap']['exec_command']
+__metaphlan2_heatmap_exec_command = config['metaphlan2_heatmap'].get('exec_command', "metaphlan_hclust_heatmap.py")
 __metaphlan2_heatmap_options = config['metaphlan2_heatmap'].get('options', "")
 
 rule heatmap:

workflows/simple_metaphlan2/README.md

+# Simple metaphlan2 workflow
+
+This is a simple example of a workflow using metaphlan2.
+
+## Example
+
+An example is provided and is based on the `config.yaml` file. Singularity images are necessary for this example as well as the samples in the appropriate folder.
\ No newline at end of file

workflows/simple_metaphlan2/SnakeFile

+configfile: "config.yaml"
+
+# ==== Rule paths ==== 
+__metaphlan2_rules = "../../tools/metaphlan2/metaphlan2/metaphlan2.rules"
+__metaphlan2_merge_rules = "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules"
+__metaphlan2_heatmap_rules = "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules"
+
+__input_dir = config['input_dir']
+__main_output_dir = config.get('output_dir', 'output')
+
+# ---- Metaphlan2
+__metaphlan2_output_dir = __main_output_dir + "/metaphlan2"
+__metaphlan2_input_type = config['metaphlan2'].get('input_type', 'fastq')
+__metaphlan2_input = "{dir}/{sample}.{ext}".format(dir=__input_dir,
+                                                   sample="{sample}",
+                                                   ext=__metaphlan2_input_type + ".gz")
+__metaphlan2_output = "{dir}/{sample}.txt".format(dir=__metaphlan2_output_dir,
+                                                  sample="{sample}")
+include: __metaphlan2_rules
+
+# ---- Metaphlan2 merge
+__metaphlan2_merge_output_dir = __main_output_dir + "/metaphlan2_merge"
+__metaphlan2_merge_output_file_name = config['metaphlan2_merge'].get('output_file_name',"merged_taxonomic_profiles.txt")
+__metaphlan2_merge_input = expand("{dir}/{sample}.txt".format(dir=__metaphlan2_output_dir,
+                                                              sample="{sample}"),
+                                  sample=config['samples'])
+__metaphlan2_merge_output = "{dir}/{file_name}".format(dir=__metaphlan2_merge_output_dir,
+                                                       file_name=__metaphlan2_merge_output_file_name) 
+include: __metaphlan2_merge_rules
+
+# ---- Metaphlan2 heatmap
+__metaphlan2_heatmap_output_dir = __main_output_dir + "/metaphlan2_heatmap"
+__metaphlan2_heatmap_output_file_name = config['metaphlan2_heatmap'].get('output_name',"heatmap.png")
+__metaphlan2_heatmap_input = __metaphlan2_merge_output
+__metaphlan2_heatmap_output = "{dir}/{file_name}".format(dir=__metaphlan2_heatmap_output_dir,
+                                                         file_name=__metaphlan2_heatmap_output_file_name) 
+include: __metaphlan2_heatmap_rules
+
+rule all:
+    input:
+        __metaphlan2_heatmap_output

workflows/simple_metaphlan2/config.yaml

+samples:
+  - SRS014459-Stool
+  - SRS014464-Anterior_nares
+  - SRS014470-Tongue_dorsum
+  - SRS014472-Buccal_mucosa
+  - SRS014476-Supragingival_plaque
+  - SRS014494-Posterior_fornix
+
+input_dir: /pasteur/homes/kehillio/Atm/kenzo/repo/workflow-benchmarking/data
+output_dir: 20190509_simplecase
+
+metaphlan2:
+  threads: 4
+  input_type: fasta
+  exec_command: singularity run --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/metaphlan2/metaphlan2.simg
+
+metaphlan2_merge:
+  exec_command: singularity run --app merge --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/metaphlan2/metaphlan2.simg 
+
+metaphlan2_heatmap:
+  exec_command: singularity run --app heatmap --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/metaphlan2/metaphlan2.simg
+  output_name: snakemake_heatmap.png