start Snakefile to extract unmapped pairs

tools/samtools/extract_unmapped_pairs/Snakefile

+__extract_unmapped_pairs_samtools_exec_command = config.get(
+    'extract_unmapped_pairs', {}
+).get('samtools_exec_command', 'samtools')
+__extract_unmapped_pairs_modules = config.get('extract_unmapped_pairs', {}).get('modules')
+
+rule extract_unmapped_pairs:
+    input:
+        __extract_unmapped_pairs_input
+    output:
+        __extract_unmapped_pairs_output
+    params:
+        exec_command = __extract_unmapped_pairs_samtools_exec_command,
+        modules = __extract_unmapped_pairs_modules,
+        options = __extract_unmapped_pairs_options
+    run:
+        command = []
+        if params.modules:
+        	command.append("module load {params.modules}")
+        command.append("{params.exec_command} view -u -f 4 -F 264 {input}  > {output}.tmps1.bam")
+        command.append("{params.exec_command} view -u -f 8 -F 260 {input}  > {output}.tmps2.bam")
+        command.append("{params.exec_command} view -u -f 12 -F 256 {input}  > {output}.tmps3.bam")
+        command.append(
+            "{params.exec_command} merge -u - {output}.tmps[123].bam | {params.exec_command} sort -n > {output}"
+        )
+        shell(" && ".join(command))