SAMTOOLS FAIDX

index reference sequence in FASTA format from reference sequence.

Example

This wrapper can be used in the following way:

rule samtools_index:
    input:
        "{sample}.fa",
    output:
        "{sample}.fa.fai",
    log:
        "{sample}.log",
    params:
        extra="",  # optional params string
    wrapper:
        "v3.8.0-1-g149ef14/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.

Notes

• The extra param allows for additional program arguments (not -o).

• For more information see, http://www.htslib.org/doc/samtools-faidx.html

Software dependencies

• samtools=1.19.2

• snakemake-wrapper-utils=0.6.2

Input/Output

Input:

• reference sequence file (.fa)

Output:

• indexed reference sequence file (.fai)

Authors

• Michael Chambers

• Filipe G. Vieira

Code

__author__ = "Michael Chambers"
__copyright__ = "Copyright 2019, Michael Chambers"
__email__ = "greenkidneybean@gmail.com"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.samtools import get_samtools_opts

samtools_opts = get_samtools_opts(
    snakemake, parse_threads=False, parse_write_index=False, parse_output_format=False
)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell("samtools faidx {samtools_opts} {extra} {snakemake.input[0]} {log}")