Commit 6cad6524 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

move bowtie2out and sams from params to output

parent 0ddcffa4
...@@ -9,13 +9,13 @@ rule metaphlan3: ...@@ -9,13 +9,13 @@ rule metaphlan3:
input: input:
__metaphlan3_input __metaphlan3_input
output: output:
__metaphlan3_output profile = __metaphlan3_output_profile,
bowtie2out = __metaphlan3_output_bowtie2out,
sams = __metaphlan3_output_sams
params: params:
exec_command = __metaphlan3_exec_command, exec_command = __metaphlan3_exec_command,
modules = __metaphlan3_modules, modules = __metaphlan3_modules,
input_type = __metaphlan3_input_type, input_type = __metaphlan3_input_type,
bowtie2out = "{output_dir}/{sample}.bowtie2.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
sams = "{output_dir}/{sample}.sam.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
options = __metaphlan3_options options = __metaphlan3_options
threads: threads:
__metaphlan3_threads __metaphlan3_threads
...@@ -23,5 +23,5 @@ rule metaphlan3: ...@@ -23,5 +23,5 @@ rule metaphlan3:
command = [] command = []
if params.modules: if params.modules:
command.append("module load {params.modules}") command.append("module load {params.modules}")
command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} -s {params.sams} --bowtie2out {params.bowtie2out} {params.options} {input} {output}") command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} -s {output.sams} --bowtie2out {output.bowtie2out} {params.options} {input} {output.profile}")
shell(" && ".join(command)) shell(" && ".join(command))
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