TABIX¶
Process given file with tabix (e.g., create index).
Software dependencies¶
- htslib ==1.10
Example¶
This wrapper can be used in the following way:
rule tabix:
input:
"{prefix}.vcf.gz"
output:
"{prefix}.vcf.gz.tbi"
params:
# pass arguments to tabix (e.g. index a vcf)
"-p vcf"
log:
"logs/tabix/{prefix}.log"
wrapper:
"0.50.4/bio/tabix"
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.
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell("tabix {snakemake.params} {snakemake.input[0]} {log}")