FGBIO ANNOTATEBAMWITHUMIS

Annotates existing BAM files with UMIs (Unique Molecular Indices, aka Molecular IDs, Molecular barcodes) from a separate FASTQ file.

URL: https://fulcrumgenomics.github.io/fgbio/

Example

This wrapper can be used in the following way:

rule annotate_bam_single_fastq:
    input:
        bam="mapped/{sample}.bam",
        umi="umi/{sample}.fastq",
    output:
        "mapped/{sample}.annotated.bam",
    params:
        "",
    resources:
        # suggestion assuming unsorted input, so that memory should
        # be proportional to input size:
        # https://fulcrumgenomics.github.io/fgbio/tools/latest/AnnotateBamWithUmis.html
        mem_mb=lambda wildcards, input: max([input.size_mb * 1.3, 200]),
    log:
        "logs/fgbio/annotate_bam/{sample}.log",
    wrapper:
        "v9.4.2/bio/fgbio/annotatebamwithumis"


rule annotate_bam_multiple_fastqs:
    input:
        bam="mapped/{sample}.bam",
        umi=[
            "umi/{sample}.fastq",
            "umi/{sample}.fastq",
        ],
    output:
        "mapped/{sample}-{sample}.annotated.bam",
    params:
        "",
    resources:
        # suggestion assuming unsorted input, so that memory should
        # be proportional to input size:
        # https://fulcrumgenomics.github.io/fgbio/tools/latest/AnnotateBamWithUmis.html
        mem_mb=lambda wildcards, input: max([input.size_mb * 1.3, 200]),
    log:
        "logs/fgbio/annotate_bam/{sample}-{sample}.log",
    wrapper:
        "v9.4.2/bio/fgbio/annotatebamwithumis"

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

• fgbio=4.0.0

• snakemake-wrapper-utils=0.8.0

Authors

• Patrik Smeds

Code

__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2018, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra_params = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

shell(
    "fgbio {java_opts} AnnotateBamWithUmis"
    " -i {snakemake.input.bam}"
    " -f {snakemake.input.umi}"
    " {extra_params}"
    " -o {snakemake.output[0]}"
    " {log}"
)