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:
        "0.65.0/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]}")