From f2052487ab7977d84f10d16ee5c6cd7d13d797b5 Mon Sep 17 00:00:00 2001 From: kehillio <kenzo-hugo.hillion1@pasteur.fr> Date: Thu, 16 May 2019 16:59:19 +0200 Subject: [PATCH] fix way to build command line --- tools/metaphlan2/metaphlan2/Snakefile | 6 ++++-- tools/metaphlan2/metaphlan2_heatmap/Snakefile | 6 ++++-- tools/metaphlan2/metaphlan2_merge/Snakefile | 6 ++++-- 3 files changed, 12 insertions(+), 6 deletions(-) diff --git a/tools/metaphlan2/metaphlan2/Snakefile b/tools/metaphlan2/metaphlan2/Snakefile index 0bee33c..4203f13 100644 --- a/tools/metaphlan2/metaphlan2/Snakefile +++ b/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)) diff --git a/tools/metaphlan2/metaphlan2_heatmap/Snakefile b/tools/metaphlan2/metaphlan2_heatmap/Snakefile index 147e0cd..46fb5c0 100644 --- a/tools/metaphlan2/metaphlan2_heatmap/Snakefile +++ b/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)) diff --git a/tools/metaphlan2/metaphlan2_merge/Snakefile b/tools/metaphlan2/metaphlan2_merge/Snakefile index d986768..d7bba93 100644 --- a/tools/metaphlan2/metaphlan2_merge/Snakefile +++ b/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)) -- GitLab