fix way to build command line

tools/metaphlan2/metaphlan2/Snakefile

@@ -16,6 +16,8 @@ rule metaphlan2:
     threads:
         __metaphlan2_threads
     run:
+        command = []
         if params.modules:
-            shell("module load {params.modules}")
-        shell("{params.exec_command} --nproc {threads} --input_type {params.input_type} {params.options} {input} {output}")
+            command.append("module load {params.modules}")
+        command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} {params.options} {input} {output}")
+        shell(" && ".join(command))

tools/metaphlan2/metaphlan2_heatmap/Snakefile

@@ -12,6 +12,8 @@ rule heatmap:
         modules = __metaphlan2_heatmap_modules,
         options = __metaphlan2_heatmap_options
     run:
+        command = []
         if params.modules:
-        	shell("module load {params.modules}")
-        shell("{params.exec_command} {params.options} --in {input} --out {output}")
+        	command.append("module load {params.modules}")
+        command.append("{params.exec_command} {params.options} --in {input} --out {output}")
+        shell(" && ".join(command))

tools/metaphlan2/metaphlan2_merge/Snakefile

@@ -12,6 +12,8 @@ rule metaphlan2_merge:
         modules = __metaphlan2_merge_modules,
         options = __metaphlan2_merge_options
     run:
+        command = []
         if params.modules:
-            shell("module load {params.modules}")
-        shell("{params.exec_command} {params.options} {input} > {output}")
+            command.append("module load {params.modules}")
+        command.append("{params.exec_command} {params.options} {input} > {output}")
+        shell(" && ".join(command))