add possibility to add modules dependencies

README.md

 # Snakemake tools and workflows
 
-This repository aims to gather all Snakemake descriptions. They all try to follow some rules in order to make them easily reusable from one workflow to another.
+This repository aims to gather Snakemake descriptions. They all try to follow some rules in order to make them easily reusable from one workflow to another.
 
 Thus, the repository is splitted in two sections:
 
 * [__tools__](tools/): All tool descriptions. These are not meant to be used directly and need to be refered in another Snakefile
-* [__subworkflows__](subworkflows/): Supposed to behave as tool descriptions, meaning that they need to be refered in another Snakefile to be used.
+* [__subworkflows__](subworkflows/): Supposed to behave as tool descriptions, meaning that they need to be refered in another Snakefile to be used
 * [__workflows__](workflows/): All workflows that are supposed to be usable directly
\ No newline at end of file

tools/metaphlan2/metaphlan2/Snakefile

-__metaphlan2_exec_command = config['metaphlan2'].get('exec_command', 'metaphlan2.py')
-__metaphlan2_options = config['metaphlan2'].get('options', "")
-__metaphlan2_threads = config['metaphlan2'].get('threads', 1)
+__metaphlan2_exec_command = config.get('metaphlan2', {}).get('exec_command', 'metaphlan2.py')
+__metaphlan2_modules = config.get('metaphlan2', {}).get('modules')
+__metaphlan2_options = config.get('metaphlan2', {}).get('options', "")
+__metaphlan2_threads = config.get('metaphlan2', {}).get('threads', 1)
 
 rule metaphlan2:
     input:
@@ -9,9 +10,12 @@ rule metaphlan2:
         __metaphlan2_output
     params:
         exec_command = __metaphlan2_exec_command,
+        modules = __metaphlan2_modules,
         input_type = __metaphlan2_input_type,
         options = __metaphlan2_options
     threads:
         __metaphlan2_threads
-    shell:
-        "{params.exec_command} --nproc {threads} --input_type {params.input_type} {params.options} {input} {output}"
+    run:
+        if params.modules:
+            shell("module load {params.modules}")
+        shell("{params.exec_command} --nproc {threads} --input_type {params.input_type} {params.options} {input} {output}")

tools/metaphlan2/metaphlan2_heatmap/Snakefile

-__metaphlan2_heatmap_exec_command = config['metaphlan2_heatmap'].get('exec_command', "metaphlan_hclust_heatmap.py")
-__metaphlan2_heatmap_options = config['metaphlan2_heatmap'].get('options', "")
+__metaphlan2_heatmap_exec_command = config.get('metaphlan2_heatmap', {}).get('exec_command', "metaphlan_hclust_heatmap.py")
+__metaphlan2_heatmap_modules = config.get('metaphlan2_heatmap', {}).get('modules')
+__metaphlan2_heatmap_options = config.get('metaphlan2_heatmap', {}).get('options', "")
 
 rule heatmap:
     input:
@@ -8,6 +9,9 @@ rule heatmap:
         __metaphlan2_heatmap_output
     params:
         exec_command = __metaphlan2_heatmap_exec_command,
+        modules = __metaphlan2_heatmap_modules,
         options = __metaphlan2_heatmap_options
-    shell:
-        "{params.exec_command} {params.options} --in {input} --out {output}"
+    run:
+        if params.modules:
+        	shell("module load {params.modules}")
+        shell("{params.exec_command} {params.options} --in {input} --out {output}")

tools/metaphlan2/metaphlan2_merge/Snakefile

-__metaphlan2_merge_exec_command = config['metaphlan2_merge'].get('exec_command', 'merge_metaphlan_tables.py')
-__metaphlan2_merge_options = config['metaphlan2_merge'].get('options', "")
+__metaphlan2_merge_exec_command = config.get('metaphlan2_merge', {}).get('exec_command', 'merge_metaphlan_tables.py')
+__metaphlan2_merge_modules = config.get('metaphlan2_merge', {}).get('modules')
+__metaphlan2_merge_options = config.get('metaphlan2_merge', {}).get('options', "")
 
 rule metaphlan2_merge:
     input:
@@ -8,6 +9,9 @@ rule metaphlan2_merge:
         __metaphlan2_merge_output
     params:
         exec_command = __metaphlan2_merge_exec_command,
+        modules = __metaphlan2_merge_modules,
         options = __metaphlan2_merge_options
-    shell:
-        "{params.exec_command} {params.options} {input} > {output}"
+    run:
+        if params.modules:
+            shell("module load {params.modules}")
+        shell("{params.exec_command} {params.options} {input} > {output}")