STRELKA GERMLINE

Call germline variants with Strelka.

Software dependencies

• strelka ==2.9.10

Example

This wrapper can be used in the following way:

rule strelka_germline:
    input:
        # the required bam file
        bam="mapped/{sample}.bam",
        # path to reference genome fasta and index
        fasta="genome.fasta",
        fasta_index="genome.fasta.fai"
    output:
        # Strelka results - either use directory or complete file path
        directory("strelka/{sample}")
    log:
        "logs/strelka/germline/{sample}.log"
    params:
        # optional parameters
        config_extra="",
        run_extra=""
    threads: 8
    wrapper:
        "0.67.0/bio/strelka/germline"

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

• Jan Forster

Code

__author__ = "Jan Forster"
__copyright__ = "Copyright 2019, Jan Forster"
__email__ = "jan.forster@uk-essen.de"
__license__ = "MIT"


import os
from pathlib import Path
from snakemake.shell import shell

config_extra = snakemake.params.get("config_extra", "")
run_extra = snakemake.params.get("run_extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

bam = snakemake.input.get("bam")  # input bam file, required
assert bam is not None, "input-> bam is a required input parameter"

if snakemake.output[0].endswith(".vcf.gz"):
    run_dir = Path(snakemake.output[0]).parents[2]
else:
    run_dir = snakemake.output

shell(
    "configureStrelkaGermlineWorkflow.py "  # configure the strelka run
    "--bam {bam} "  # input bam
    "--referenceFasta {snakemake.input.fasta} "  # reference genome
    "--runDir {run_dir} "  # output directory
    "{config_extra} "  # additional parameters for the configuration
    "&& {run_dir}/runWorkflow.py "  # run the strelka workflow
    "-m local "  # run in local mode
    "-j {snakemake.threads} "  # number of threads
    "{run_extra} "  # additional parameters for the run
    "{log}"
)  # logging