PICARD COLLECTINSERTSIZEMETRICS

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

Collect metrics on insert size of paired end reads with picard tools.

Example

This wrapper can be used in the following way:

rule insert_size:
    input:
        "mapped/{sample}.bam",
    output:
        txt="stats/{sample}.isize.txt",
        pdf="stats/{sample}.isize.pdf",
    log:
        "logs/picard/insert_size/{sample}.log",
    params:
        # optional parameters (e.g. relax checks as below)
        extra="--VALIDATION_STRINGENCY LENIENT --METRIC_ACCUMULATION_LEVEL null --METRIC_ACCUMULATION_LEVEL SAMPLE",
    # 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:
        "v3.12.1-18-g9861c57/bio/picard/collectinsertsizemetrics"

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

  • r-base=4.4.1

  • snakemake-wrapper-utils=0.6.2

Input/Output

Input:

  • bam file

Output:

  • txt: textual representation of metrics

  • pdf: insert size histogram

Authors

  • Johannes Köster

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "johannes.koester@protonmail.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 CollectInsertSizeMetrics"
        " {java_opts} {extra}"
        " --INPUT {snakemake.input}"
        " --TMP_DIR {tmpdir}"
        " --OUTPUT {snakemake.output.txt}"
        " --Histogram_FILE {snakemake.output.pdf}"
        " {log}"
    )