diff --git a/tools/metaphlan3/metaphlan/paired/Snakefile b/tools/metaphlan3/metaphlan/paired/Snakefile index 3e41c2fea8911663a5bb2185f4e8cc011e436fe3..55175901ad8cbe8aeb75453808d1b82196aa7810 100644 --- a/tools/metaphlan3/metaphlan/paired/Snakefile +++ b/tools/metaphlan3/metaphlan/paired/Snakefile @@ -18,13 +18,13 @@ rule metaphlan3_paired: r1 = __metaphlan3_input_r1, r2 = __metaphlan3_input_r2 output: - __metaphlan3_output + profile = __metaphlan3_output, + bowtie2out = __metaphlan3_output_bowtie2out, + sams = __metaphlan3_output_sams params: exec_command = __metaphlan3_exec_command, 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 @@ -32,5 +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} -s {params.sams} --bowtie2out {params.bowtie2out} {params.options} {input.r1},{input.r2} {output}") + command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} -s {output.sams} --bowtie2out {output.bowtie2out} {params.options} {input.r1},{input.r2} {output.profile}") shell(" && ".join(command))