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wrapper.py
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wrapper.py
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__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2021, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com"
__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)
aln = snakemake.input.get("aln", "")
if aln:
aln = f"--input {aln}"
contamination = snakemake.input.get("contemination_table", "")
if contamination:
contamination = f"--contamination-table {contamination}"
segmentation = snakemake.input.get("segmentation", "")
if segmentation:
segmentation = f"--tumor-segmentation {segmentation}"
f1r2 = snakemake.input.get("f1r2", "")
if f1r2:
f1r2 = f"--orientation-bias-artifact-priors {f1r2}"
intervals = snakemake.input.get("bed", "")
if intervals:
intervals = f"--intervals {intervals}"
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"gatk --java-options '{java_opts}' FilterMutectCalls"
" --variant {snakemake.input.vcf}"
" --reference {snakemake.input.ref}"
" {aln}" # BAM/SAM/CRAM file containing reads
" {contamination}" # Tables containing contamination information
" {segmentation}" # Tumor segments' minor allele fractions
" {f1r2}" # .tar.gz files containing tables of prior artifact
" {intervals}" # Genomic intervals over which to operate
" {extra}"
" --tmp-dir {tmpdir}"
" --output {snakemake.output.vcf}"
" {log}"
)