__author__ = "Johannes Köster" __copyright__ = "Copyright 2016, Johannes Köster" __email__ = "*****@*****.**" __license__ = "MIT" from snakemake.shell import shell from snakemake_wrapper_utils.bcftools import get_bcftools_opts bcftools_opts = get_bcftools_opts(snakemake) extra = snakemake.params.get("extra", "") log = snakemake.log_fmt_shell(stdout=True, stderr=True) shell("bcftools view {bcftools_opts} " "{extra} " "{snakemake.input[0]} " "-o {snakemake.output} " "{log}")
__author__ = "Patrik Smeds" __copyright__ = "Copyright 2021, Patrik Smeds" __email__ = "*****@*****.**" __license__ = "MIT" from snakemake.shell import shell from snakemake_wrapper_utils.bcftools import get_bcftools_opts bcftools_opts = get_bcftools_opts(snakemake, parse_memory=False) log = snakemake.log_fmt_shell(stdout=False, stderr=True) if len(snakemake.output) > 1: raise Exception("Only one output file expected, got: " + str(len(snakemake.output))) filter = snakemake.params.get("filter", "") extra = snakemake.params.get("extra", "") shell("bcftools filter {filter} {extra} {snakemake.input[0]} " "{bcftools_opts} " "-o {snakemake.output[0]} " "{log}")