PICARD REVERTSAM

Reverts SAM or BAM files to a previous state. .

Software dependencies

• picard ==2.22.1

Example

This wrapper can be used in the following way:

rule revert_bam:
    input:
        "mapped/{sample}.bam"
    output:
        "revert/{sample}.bam"
    log:
        "logs/picard/revert_sam/{sample}.log"
    params:
        extra="SANITIZE=true" # optional: Extra arguments for picard.
    wrapper:
        "0.56.0/bio/picard/revertsam"

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

• Patrik Smeds

Code

"""Snakemake wrapper for picard RevertSam."""

__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2018, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"


from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

shell(
    "picard"
    " RevertSam"
    " {extra}"
    " INPUT={snakemake.input[0]}"
    " OUTPUT={snakemake.output[0]}"
    " {log}"
)