Commit 491d5f1c authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

add sams output from metaphlan3

parent 4134975f
...@@ -14,7 +14,8 @@ rule metaphlan3: ...@@ -14,7 +14,8 @@ rule metaphlan3:
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}"), bowtie2out = "{output_dir}/bowtie2/{sample}.bowtie2.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
sams = "{output_dir}/sams/{sample}.sam.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
options = __metaphlan3_options options = __metaphlan3_options
threads: threads:
__metaphlan3_threads __metaphlan3_threads
...@@ -22,5 +23,5 @@ rule metaphlan3: ...@@ -22,5 +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} --bowtie2out {params.bowtie2out} {params.options} {input} {output}") command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} -s {params.sams} --bowtie2out {params.bowtie2out} {params.options} {input} {output}")
shell(" && ".join(command)) shell(" && ".join(command))
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