PICARD COLLECTGCBIASMETRICS

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

Run picard CollectGcBiasMetrics to generate QC metrics pertaining to GC bias.

Example

This wrapper can be used in the following way:

rule alignment_summary:
    input:
        # BAM aligned to reference genome
        bam="mapped/a.bam",
        # reference genome FASTA from which GC-context is inferred
        ref="genome.fasta",
    output:
        metrics="results/a.gcmetrics.txt",
        chart="results/a.gc.pdf",
        summary="results/a.summary.txt",
    params:
        # optional additional parameters, for example,
        extra="--MINIMUM_GENOME_FRACTION 1E-5",
    log:
        "logs/picard/a.gcmetrics.log",
    # 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/collectgcbiasmetrics"

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

Input/Output

Input:

  • BAM file of RNA-seq data aligned to genome

  • REF_FLAT formatted file of transcriptome annotations

Output:

  • GC metrics text file

  • GC metrics PDF figure

  • GC summary metrics text file

Authors

  • Brett Copeland

Code

__author__ = "Brett Copeland"
__copyright__ = "Copyright 2021, Brett Copeland"
__email__ = "brcopeland@ucsd.edu"
__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 CollectGcBiasMetrics"
        " {java_opts} {extra}"
        " --INPUT {snakemake.input.bam}"
        " --TMP_DIR {tmpdir}"
        " --OUTPUT {snakemake.output.metrics}"
        " --CHART {snakemake.output.chart}"
        " --SUMMARY_OUTPUT {snakemake.output.summary}"
        " --REFERENCE_SEQUENCE {snakemake.input.ref}"
        " {log}"
    )