bwa bwa aln

bwa aln

Version:
0.7.x
Identifier: TL_a6be17_b3.8e
Tool
1"""Snakemake wrapper for bwa aln."""
2# Snakemake wrappers are provided by Truwl to teach the internal mechanics of Snakemake recipes. View https://github.com/snakemake/snakemake-wrappers to learn how to use wrappers.
3
4__author__ = "Julian de Ruiter"
5__copyright__ = "Copyright 2017, Julian de Ruiter"
6__email__ = "julianderuiter@gmail.com"
7__license__ = "MIT"
8
9
10from snakemake.shell import shell
11
12
13extra = snakemake.params.get("extra", "")
14log = snakemake.log_fmt_shell(stdout=False, stderr=True)
15
16shell(
17    "bwa aln"
18    " {extra}"
19    " -t {snakemake.threads}"
20    " {snakemake.params.index}"
21    " {snakemake.input[0]}"
22    " > {snakemake.output[0]} {log}"
23)
24