add sams output to paired metaphlan

tools/metaphlan3/metaphlan/paired/Snakefile

@@ -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))

tools/metaphlan3/metaphlan/single/Snakefile

@@ -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