update extract of unmapped pairs with samtools

tools/samtools/extract_unmapped_pairs/Snakefile

@@ -10,8 +10,7 @@ rule extract_unmapped_pairs:
         __extract_unmapped_pairs_output
     params:
         exec_command = __extract_unmapped_pairs_samtools_exec_command,
-        modules = __extract_unmapped_pairs_modules,
-        options = __extract_unmapped_pairs_options
+        modules = __extract_unmapped_pairs_modules
     run:
         command = []
         if params.modules:
@@ -22,4 +21,5 @@ rule extract_unmapped_pairs:
         command.append(
             "{params.exec_command} merge -u - {output}.tmps[123].bam | {params.exec_command} sort -n > {output}"
         )
+        command.append("rm {output}.tmps[123].bam")
         shell(" && ".join(command))

tools/samtools/extract_unmapped_pairs/example_usage/Snakefile

@@ -10,12 +10,9 @@ SAMPLES = config.get('samples')
 __input_dir = config.get('input_dir', 'data')
 
 # ==== Extract unmapped pairs ====
-__extract_unmapped_pairs_input = expand(
-    "{dir}/{{sample}}.bam".format(dir=__input_dir), sample=SAMPLES
-)
-__extract_unmapped_pairs_output = expand(
-    "{dir}/{{sample}}_unmapped.bam".format(dir=__input_dir), sample=SAMPLES
-)
+__extract_unmapped_pairs_output_dir = f"{__main_output_dir}/extract_unmapped_pairs"
+__extract_unmapped_pairs_input = "{dir}/{{sample}}.bam".format(dir=__input_dir, sample="{sample}")
+__extract_unmapped_pairs_output = "{dir}/{{sample}}_unmapped.bam".format(dir=__extract_unmapped_pairs_output_dir, sample="{sample}")
 include: __extract_unmapped_pairs_rules
 
 rule all: