<reponame>avilab/vs-wrappers<filename>bbtools/shred/wrapper.py
__author__ = "<NAME>"
__copyright__ = "Copyright 2019, <NAME>"
__email__ = "<EMAIL>"
__license__ = "MIT"

from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts


java_opts = get_java_opts(snakemake)

# Get extra arguments
extra = snakemake.params.get("extra", "")

# Setup log
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

# Run commands
shell(
    "(shred.sh in={snakemake.input[0]} out={snakemake.output[0]} {extra} {java_opts}) {log}"
)

__author__ = "<NAME>"
__copyright__ = "Copyright 2019, <NAME>"
__email__ = "<EMAIL>"
__license__ = "MIT"

from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts


java_opts = get_java_opts(snakemake)

# Get extra arguments
extra = snakemake.params.get("extra", "")

# Setup log
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

# Run commands
shell(
    "(shred.sh in={snakemake.input[0]} out={snakemake.output[0]} {extra} {java_opts}) {log}"
)
# Get extra arguments # Setup log # Run commands