PICARD COLLECTTARGETEDPCRMETRICS

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Collect metric information for target pcr metrics runs, with picard tools.

Example

This wrapper can be used in the following way:

rule CollectTargetedPcrMetrics:
    input:
        bam="mapped/{sample}.bam",
        amplicon_intervals="amplicon.interval_list",
        target_intervals="target.interval_list",
    output:
        "stats/{sample}.pcr.txt",
    log:
        "logs/picard/collecttargetedpcrmetrics/{sample}.log",
    params:
        extra="",
    # optional specification of memory usage of the JVM that snakemake will respect with global
    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
    resources:
        mem_mb=1024,
    wrapper:
        "v3.8.0-1-g149ef14/bio/picard/collecttargetedpcrmetrics"

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

Software dependencies

  • picard=3.1.1

  • snakemake-wrapper-utils=0.6.2

Authors

  • Patrik Smeds

Code

__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2019, Patrik Smeds"
__email__ = "patrik.smeds@mail.com"
__license__ = "MIT"


import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts


log = snakemake.log_fmt_shell()

extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "picard CollectTargetedPcrMetrics"
        " {java_opts} {extra}"
        " --INPUT {snakemake.input.bam}"
        " --TMP_DIR {tmpdir}"
        " --OUTPUT {snakemake.output[0]}"
        " --AMPLICON_INTERVALS {snakemake.input.amplicon_intervals}"
        " --TARGET_INTERVALS {snakemake.input.target_intervals}"
        " {log}"
    )