FGBIO GROUPREADSBYUMI

Groups reads together that appear to have come from the same original molecule.

Software dependencies

  • fgbio ==0.6.1

Example

This wrapper can be used in the following way:

rule GroupReads:
    input:
        "mapped/a.bam"
    output:
        "mapped/{sample}.gu.bam"
    params:
        extra="-s adjacency --edits 1"
    log:
        "logs/fgbio/group_reads/{sample}.log"
    wrapper:
        "0.31.1/bio/fgbio/groupreadsbyumi"

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.

Authors

  • Patrik Smeds

Code

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


from snakemake.shell import shell

shell.executable("bash")

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

extra_params = snakemake.params.get("extra", "")

bam_input = snakemake.input[0]

if not isinstance(bam_input, str) and len(snakemake.input) != 1:
    raise ValueError("Input bam should be one bam file: " + str(bam_input) + "!")

output_file = snakemake.output[0]

if not isinstance(output_file, str) and len(snakemake.output) != 1:
    raise ValueError("Output should be one bam file: " + str(output_file) + "!")

shell("fgbio GroupReadsByUmi"
      " -i {bam_input}"
      " -o {output_file}"
      " {extra_params}"
      " {log}")