jannovar jannovar __main__

jannovar __main__

Version:
0.31
Identifier: TL_593213_54.ba
Tool
1__author__ = "Bradford Powell"
2__copyright__ = "Copyright 2018, Bradford Powell"
3__email__ = "bpow@unc.edu"
4__license__ = "BSD"
5
6
7from snakemake.shell import shell
8from snakemake_wrapper_utils.java import get_java_opts
9
10shell.executable("bash")
11
12log = snakemake.log_fmt_shell(stdout=False, stderr=True)
13
14extra = snakemake.params.get("extra", "")
15java_opts = get_java_opts(snakemake)
16
17pedigree = snakemake.input.get("pedigree", "")
18if pedigree:
19    pedigree = '--pedigree-file "%s"' % pedigree
20
21shell(
22    "jannovar annotate-vcf --database {snakemake.params.database}"
23    " --input-vcf {snakemake.input.vcf} --output-vcf {snakemake.output}"
24    " {pedigree} {extra} {java_opts} {log}"
25)
26