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wrapper.py
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wrapper.py
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__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2022, Filipe G. Vieira"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
input = snakemake.input.get("aln", "")
if input:
input = f"--input {input}"
reference = snakemake.input.get("ref", "")
if reference:
reference = f"--reference {reference}"
dbsnp = snakemake.input.get("known", "")
if dbsnp:
dbsnp = f"--dbsnp {dbsnp}"
intervals = snakemake.input.get("intervals", "")
if not intervals:
intervals = snakemake.params.get("intervals", "")
if intervals:
intervals = "--intervals {}".format(intervals)
resources = [
f"--resource:{name} {file}"
for name, file in snakemake.input.items()
if name not in ["vcf", "aln", "ref", "known", "intervals", "bai"]
]
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"gatk --java-options '{java_opts}' VariantAnnotator"
" --variant {snakemake.input.vcf}"
" {input}"
" {reference}"
" {dbsnp}"
" {intervals}"
" {resources}"
" {extra}"
" --tmp-dir {tmpdir}"
" --output {snakemake.output.vcf}"
" {log}"
)