PICARD COLLECTMULTIPLEMETRICS

A picard meta-metrics tool that collects multiple classes of metrics. You can select which tool(s) to run by adding the respective extension(s) (see table below) to the requested output of the wrapper invocation (see example Snakemake rule below).

Tool	Extension(s) for the output files
CollectAlignmentSummaryMetrics	.alignment_summary_metrics
CollectInsertSizeMetrics	.insert_size_metrics, .insert_size_histogram.pdf
QualityScoreDistribution	.quality_distribution_metrics, .quality_distribution.pdf
MeanQualityByCycle	.quality_by_cycle_metrics, .quality_by_cycle.pdf
CollectBaseDistributionByCycle	.base_distribution_by_cycle_metrics, .base_distribution_by_cycle.pdf
CollectGcBiasMetrics	.gc_bias.detail_metrics, .gc_bias.summary_metrics, .gc_bias.pdf
RnaSeqMetrics	.rna_metrics
CollectSequencingArtifactMetrics	.bait_bias_detail_metrics, .bait_bias_summary_metrics, .error_summary_metrics, .pre_adapter_detail_metrics, .pre_adapter_summary_metrics
CollectQualityYieldMetrics	.quality_yield_metrics

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

Example

This wrapper can be used in the following way:

rule collect_multiple_metrics:
    input:
        bam="mapped/{sample}.bam",
        ref="genome.fasta",
    output:
        # Through the output file extensions the different tools for the metrics can be selected
        # so that it is not necessary to specify them under params with the "PROGRAM" option.
        # Usable extensions (and which tools they implicitly call) are listed here:
        #         https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/picard/collectmultiplemetrics.html.
        multiext(
            "stats/{sample}",
            ".alignment_summary_metrics",
            ".insert_size_metrics",
            ".insert_size_histogram.pdf",
            ".quality_distribution_metrics",
            ".quality_distribution.pdf",
            ".quality_by_cycle_metrics",
            ".quality_by_cycle.pdf",
            ".base_distribution_by_cycle_metrics",
            ".base_distribution_by_cycle.pdf",
            ".gc_bias.detail_metrics",
            ".gc_bias.summary_metrics",
            ".gc_bias.pdf",
            ".rna_metrics",
            ".bait_bias_detail_metrics",
            ".bait_bias_summary_metrics",
            ".error_summary_metrics",
            ".pre_adapter_detail_metrics",
            ".pre_adapter_summary_metrics",
            ".quality_yield_metrics",
        ),
    # 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=4096,
    log:
        "logs/picard/multiple_metrics/{sample}.log",
    params:
        # optional parameters
        # REF_FLAT is required if RnaSeqMetrics are used
        extra="--VALIDATION_STRINGENCY LENIENT --METRIC_ACCUMULATION_LEVEL null --METRIC_ACCUMULATION_LEVEL SAMPLE --REF_FLAT ref_flat.txt",
    wrapper:
        "v3.8.0/bio/picard/collectmultiplemetrics"

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 (.bam)

• FASTA reference sequence file (.fasta or .fa)

Output:

• multiple metrics text files (_metrics) AND

• multiple metrics pdf files (.pdf)

• the appropriate extensions for the output files must be used depending on the desired tools

Authors

• David Laehnemann

• Antonie Vietor

• Filipe G. Vieira

Code

__author__ = "David Laehnemann, Antonie Vietor"
__copyright__ = "Copyright 2020, David Laehnemann, Antonie Vietor"
__email__ = "antonie.v@gmx.de"
__license__ = "MIT"

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

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

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

exts_to_prog = {
    ".alignment_summary_metrics": "CollectAlignmentSummaryMetrics",
    ".insert_size_metrics": "CollectInsertSizeMetrics",
    ".insert_size_histogram.pdf": "CollectInsertSizeMetrics",
    ".quality_distribution_metrics": "QualityScoreDistribution",
    ".quality_distribution.pdf": "QualityScoreDistribution",
    ".quality_by_cycle_metrics": "MeanQualityByCycle",
    ".quality_by_cycle.pdf": "MeanQualityByCycle",
    ".base_distribution_by_cycle_metrics": "CollectBaseDistributionByCycle",
    ".base_distribution_by_cycle.pdf": "CollectBaseDistributionByCycle",
    ".gc_bias.detail_metrics": "CollectGcBiasMetrics",
    ".gc_bias.summary_metrics": "CollectGcBiasMetrics",
    ".gc_bias.pdf": "CollectGcBiasMetrics",
    ".rna_metrics": "RnaSeqMetrics",
    ".bait_bias_detail_metrics": "CollectSequencingArtifactMetrics",
    ".bait_bias_summary_metrics": "CollectSequencingArtifactMetrics",
    ".error_summary_metrics": "CollectSequencingArtifactMetrics",
    ".pre_adapter_detail_metrics": "CollectSequencingArtifactMetrics",
    ".pre_adapter_summary_metrics": "CollectSequencingArtifactMetrics",
    ".quality_yield_metrics": "CollectQualityYieldMetrics",
}


# Select programs to run from output files
progs = set()
for file in snakemake.output:
    matched = False
    for ext in exts_to_prog:
        if file.endswith(ext):
            progs.add(exts_to_prog[ext])
            matched = True
    if not matched:
        raise ValueError(
            "Unknown type of metrics file requested, for possible metrics files, see https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/picard/collectmultiplemetrics.html"
        )

programs = "--PROGRAM null --PROGRAM " + " --PROGRAM ".join(progs)


# Infer common output prefix
output_file = str(snakemake.output[0])
for ext in exts_to_prog:
    if output_file.endswith(ext):
        out = output_file[: -len(ext)]
        break


with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "picard CollectMultipleMetrics"
        " {java_opts} {extra}"
        " --INPUT {snakemake.input.bam}"
        " --TMP_DIR {tmpdir}"
        " --OUTPUT {out}"
        " --REFERENCE_SEQUENCE {snakemake.input.ref}"
        " {programs}"
        " {log}"
    )


# Under some circumstances, some picard programs might not produce an output (https://github.com/snakemake/snakemake-wrappers/issues/357). To avoid snakemake errors, the output files of those programs are created empty (if they do not exist).
for ext in [
    ext for ext, prog in exts_to_prog.items() if prog in ["CollectInsertSizeMetrics"]
]:
    for file in snakemake.output:
        if file.endswith(ext) and not Path(file).is_file():
            Path(file).touch()