MSISENSOR SCAN

Scan homopolymers and microsatelites with MSIsensor

Example

This wrapper can be used in the following way:

rule test_msisensor_scan:
    input:
        "genome.fasta"
    output:
        "microsat.list"
    message:
        "Testing MSISensor scan"
    threads:
        1
    params:
        extra = ""
    log:
        "logs/msisensor_scan.log"
    wrapper:
        "v3.0.1-5-gc155ca9/bio/msisensor/scan"

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.

Software dependencies

• msisensor=0.5

Input/Output

Input:

• A (multi)fasta formatted file

Output:

• A text file containing homopolymers and microsatelites

Authors

• Thibault Dayris

Code

"""Snakemake script for MSISensor Scan"""

__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2020, Dayris Thibault"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

# Extra parameters default value is an empty string
extra = snakemake.params.get("extra", "")

shell(
    "msisensor scan "  # Tool and its sub-command
    "-d {snakemake.input} "  # Path to fasta file
    "-o {snakemake.output} "  # Path to output file
    "{extra} "  # Optional extra parameters
    "{log}"  # Logging behavior
)