PICARD SORTSAM

Sort sam/bam files using picard tools.

Software dependencies

  • picard ==2.22.1

Example

This wrapper can be used in the following way:

rule sort_bam:
    input:
        "mapped/{sample}.bam"
    output:
        "sorted/{sample}.bam"
    log:
        "logs/picard/sort_sam/{sample}.log"
    params:
        sort_order="coordinate",
        extra="VALIDATION_STRINGENCY=LENIENT" # optional: Extra arguments for picard.
    wrapper:
        "0.50.4/bio/picard/sortsam"

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

  • Julian de Ruiter

Code

"""Snakemake wrapper for picard SortSam."""

__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@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"
    " SortSam"
    " {extra}"
    " INPUT={snakemake.input[0]}"
    " OUTPUT={snakemake.output[0]}"
    " SORT_ORDER={snakemake.params.sort_order}"
    " {log}"
)