GATK GENOMICSDBIMPORT¶
Run gatk GenomicsDBImport.
Example¶
This wrapper can be used in the following way:
rule genomics_db_import:
input:
gvcfs=["calls/a.g.vcf.gz", "calls/b.g.vcf.gz"],
output:
db=directory("db"),
log:
"logs/gatk/genomicsdbimport.log"
params:
intervals="ref",
db_action="create", # optional
extra="", # optional
java_opts="", # optional
resources:
mem_mb=1024
wrapper:
"0.74.0/bio/gatk/genomicsdbimport"
Note that input, output and log file paths can be chosen freely. When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Software dependencies¶
gatk4==4.2.0.0
snakemake-wrapper-utils==0.1.3
Notes¶
- The java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-XX:ParallelGCThreads=10” (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).
- The intervals param is mandatory
- By default, the wrapper will create a new database (output directory must be empty or non-existent). If you want to update an existing DB, set db_action param to update.
- The extra param alllows for additional program arguments.
- For more inforamtion see, https://gatk.broadinstitute.org/hc/en-us/articles/360051305591-GenomicsDBImport
Authors¶
- Filipe G. Vieira
Code¶
__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2021, Filipe G. Vieira"
__license__ = "MIT"
import os
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)
gvcfs = list(map("--variant {}".format, snakemake.input.gvcfs))
db_action = snakemake.params.get("db_action", "create")
if db_action == "create":
db_action = "--genomicsdb-workspace-path"
elif db_action == "update":
db_action = "--genomicsdb-update-workspace-path"
else:
raise ValueError(
"invalid option provided to 'params.db_action'; please choose either 'create' or 'update'."
)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"gatk --java-options '{java_opts}' GenomicsDBImport {extra} "
"{gvcfs} "
"--intervals {snakemake.params.intervals} "
"{db_action} {snakemake.output.db} {log}"
)