Commit 0ddcffa4 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

add sams output to paired metaphlan

parent d1e501f6
......@@ -24,6 +24,7 @@ rule metaphlan3_paired:
modules = __metaphlan3_modules,
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
threads:
__metaphlan3_threads
......@@ -31,5 +32,5 @@ rule metaphlan3_paired:
command = []
if 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.r1},{input.r2} {output}")
command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} -s {params.sams} --bowtie2out {params.bowtie2out} {params.options} {input.r1},{input.r2} {output}")
shell(" && ".join(command))
......@@ -15,7 +15,7 @@ rule metaphlan3:
modules = __metaphlan3_modules,
input_type = __metaphlan3_input_type,
bowtie2out = "{output_dir}/{sample}.bowtie2.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
sams = "{output_dir}/{sample}.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
threads:
__metaphlan3_threads
......
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