move bowtie2out and sams from params to output

tools/metaphlan3/metaphlan/single/Snakefile

@@ -9,13 +9,13 @@ rule metaphlan3:
     input:
         __metaphlan3_input
     output:
-        __metaphlan3_output
+        profile = __metaphlan3_output_profile,
+        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
@@ -23,5 +23,5 @@ rule metaphlan3:
         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} {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))