PICARD COLLECTRNASEQMETRICS

Run picard CollectRnaSeqMetrics to generate QC metrics for RNA-seq data.

URL:

Example

This wrapper can be used in the following way:

rule alignment_summary:
    input:
        # BAM aligned, splicing-aware, to reference genome
        bam="mapped/a.bam",
        # Annotation file containing transcript, gene, and exon data
        refflat="annotation.refFlat",
    output:
        "results/a.rnaseq_metrics.txt",
    params:
        # strand is optional (defaults to NONE) and pertains to the library preparation
        # options are FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND, and NONE
        strand="NONE",
        # optional additional parameters, for example,
        extra="--VALIDATION_STRINGENCY STRICT",
    log:
        "logs/picard/rnaseq-metrics/a.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:
        "v1.2.1/bio/picard/collectrnaseqmetrics"

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.

Software dependencies

• picard=2.26
• snakemake-wrapper-utils==0.1.3

Input/Output

Input:

• BAM file of RNA-seq data aligned to genome
• REF_FLAT formatted file of transcriptome annotations

Output:

• RNA-Seq metrics text file

Notes

• The java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-XX:ParallelGCThreads=10” (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).
• The extra param allows for additional program arguments.
• –TMP_DIR is automatically set by resources.tmpdir
• For more information, see https://broadinstitute.github.io/picard/command-line-overview.html#CollectRnaSeqMetrics

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()

strand = snakemake.params.get("strand", "NONE")
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)


with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "picard CollectRnaSeqMetrics"
        " {java_opts} {extra}"
        " --INPUT {snakemake.input.bam}"
        " --TMP_DIR {tmpdir}"
        " --OUTPUT {snakemake.output}"
        " --REF_FLAT {snakemake.input.refflat}"
        " --STRAND_SPECIFICITY {strand}"
        " {log}"
    )