SAMBAMBA VIEW

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

Filter and/or view BAM files. See details `here https://lomereiter.github.io/sambamba/docs/sambamba-view.html`_

Example

This wrapper can be used in the following way:

rule sambamba_view:
    input:
        "mapped/{sample}.bam"
    output:
        "mapped/{sample}.filtered.bam"
    params:
        extra="-f bam -F 'mapping_quality >= 50'"  # optional parameters
    log:
        "logs/sambamba-view/{sample}.log"
    threads: 8
    wrapper:
        "v3.10.2-32-gf4e5b66/bio/sambamba/view"

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

  • sambamba=1.0

Input/Output

Input:

  • bam/sam file

Output:

  • (filtered) bam/sam file

Authors

  • Jan Forster

Code

__author__ = "Jan Forster"
__copyright__ = "Copyright 2021, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"


import os

from snakemake.shell import shell

in_file = snakemake.input[0]
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

if in_file.endswith(".sam") and ("-S" not in extra or "--sam-input" not in extra):
    extra += " --sam-input"

shell(
    "sambamba view {extra} -t {snakemake.threads} "
    "{snakemake.input[0]} > {snakemake.output[0]} "
    "{log}"
)