MSISENSOR SCAN¶
Scan homopolymers and microsatelites with MSIsensor
URL:
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:
"0.80.1/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
)