BAMTOOLS FILTER WITH JSON

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/bamtools/filter_json?label=version%20update%20pull%20requests

Filters BAM files with JSON-script for filtering parameters and rules. For more information about bamtools see bamtools documentation

URL: https://github.com/pezmaster31/bamtools

Example

This wrapper can be used in the following way:

rule bamtools_filter_json:
    input:
        "{sample}.bam"
    output:
        "filtered/{sample}.bam"
    params:
        json="filtering-rules.json",
        region="" # optional parameter for defining a specific region, e.g. "chr1:500..chr3:750"
    log:
        "logs/bamtools/filtered/{sample}.log"
    wrapper:
        "v3.8.0-1-g149ef14/bio/bamtools/filter_json"

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

A complete usage documentation is available here: https://raw.githubusercontent.com/wiki/pezmaster31/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf

This tool/wrapper does not handle multi threading

Software dependencies

  • bamtools=2.5.2

Input/Output

Input:

  • bam files (.bam), must be in first position

Output:

  • bam file (.bam), must be in first position

Params

  • json: Path to filter file, json formatted.

  • region: see documentation for more information about multiple formats.

Authors

  • Antonie Vietor

Code

__author__ = "Antonie Vietor"
__copyright__ = "Copyright 2020, Antonie Vietor"
__email__ = "antonie.v@gmx.de"
__license__ = "MIT"

from snakemake.shell import shell

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

region = snakemake.params.get("region")
region_param = ""

if region and region is not None:
    region_param = ' -region "' + region + '"'

shell(
    "(bamtools filter"
    " -in {snakemake.input[0]}"
    " -out {snakemake.output[0]}"
    + region_param
    + " -script {snakemake.params.json}) {log}"
)