Commit f2052487 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

fix way to build command line

parent bc228c62
......@@ -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))
......@@ -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))
......@@ -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))
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