SAMTOOLS FAIDX¶
index reference sequence in FASTA format from reference sequence
Software dependencies¶
- samtools ==1.10
Example¶
This wrapper can be used in the following way:
rule samtools_index:
input:
"{sample}.fa"
output:
"{sample}.fa.fai"
params:
"" # optional params string
wrapper:
"0.62.0/bio/samtools/faidx"
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¶
- Michael Chambers
Code¶
__author__ = "Michael Chambers"
__copyright__ = "Copyright 2019, Michael Chambers"
__email__ = "greenkidneybean@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
shell("samtools faidx {snakemake.params} {snakemake.input[0]} > {snakemake.output[0]}")