add graphlan to metaphlan2 workflow

workflows/simple_metaphlan2/SnakeFile

@@ -4,6 +4,7 @@ configfile: "config.yaml"
 __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"
+__graphlan_from_metaphlan2_rules = "../subworkflows/graphlan_from_metaphlan2/SnakeFile"
 
 __input_dir = config['input_dir']
 __main_output_dir = config.get('output_dir', 'output')
@@ -36,6 +37,15 @@ __metaphlan2_heatmap_output = "{dir}/{file_name}".format(dir=__metaphlan2_heatma
                                                          file_name=__metaphlan2_heatmap_output_file_name) 
 include: __metaphlan2_heatmap_rules
 
+# ---- Graphlan Dendogram
+__graphlan_from_metaphlan2_output_dir = __main_output_dir + "/graphlan"
+__graphlan_from_metaphlan2_output_file_name = config['graphlan_from_metaphlan2'].get('output_name',"dendogram.png")
+__graphlan_from_metaphlan2_input = __metaphlan2_merge_output
+__graphlan_from_metaphlan2_output = "{dir}/{file_name}".format(dir=__graphlan_from_metaphlan2_output_dir,
+                                                         file_name=__graphlan_from_metaphlan2_output_file_name) 
+include: __graphlan_from_metaphlan2_rules
+
 rule all:
     input:
-        __metaphlan2_heatmap_output
+        heatmap: __metaphlan2_heatmap_output,
+        dendogram: __graphlan_from_metaphlan2_output

workflows/simple_metaphlan2/config.yaml

@@ -20,3 +20,14 @@ metaphlan2_merge:
 metaphlan2_heatmap:
   exec_command: singularity run --app heatmap --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/metaphlan2/metaphlan2.simg
   output_name: snakemake_heatmap.png
+
+export2graphlan:
+  exec_command: singularity run --app export2graphlan --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/graphlan/graphlan.simg
+  options: "--skip_rows 1,2 --most_abundant 100 --abundance_threshold 1 --least_biomarkers 10 --annotations 5,6 --external_annotations 7 --min_clade_size 1"
+
+graphlan_annotate:
+  exec_command: singularity run --app graphlan_annotate --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/graphlan/graphlan.simg
+
+graphlan:
+  exec_command: singularity run --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/graphlan/graphlan.simg
+  options: "--dpi 300 --external_legends"
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