PICARD COLLECTRNASEQMETRICS

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

URL: https://broadinstitute.github.io/picard/command-line-overview.html#CollectRnaSeqMetrics

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",
    # Reference genome
        #ref="ref.fasta",
        # 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",
    resources:
        mem_mb=1024,
    wrapper:
        "v3.8.0-1-g149ef14/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.

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

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

  • reference FASTA (optional)

Output:

  • RNA-Seq metrics text file

Authors

  • Brett Copeland

  • Filipe G. Vieira

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)


ref = snakemake.input.get("ref", "")
if ref:
    ref = f"--REFERENCE_SEQUENCE {ref}"


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