BUSTOOLS SORT

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/bustools/sort?label=version%20update%20pull%20requests

Sort raw BUS output from pseudoalignment programs

URL: https://github.com/BUStools/bustools#sort

Example

This wrapper can be used in the following way:

rule test_bustools_sort:
    input:
        "file.bus",
    output:
        "sorted.bus",
    threads: 1
    resources:
        mem_mb=765,
    params:
        extra="--umi",
    log:
        "bustools.log",
    wrapper:
        "v1.20.0-15-g28df43c2/bio/bustools/sort"

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

–temp is automatically defined through resources.tmpdir

–memory is automatically defined through resources.mem_mb

Multiple bus files in input will result in a single bus file in output.

Software dependencies

  • bustools=0.41.0
  • snakemake-wrapper-utils=0.5.0

Input/Output

Input:

  • Path to bus file, or list of bus files

Output:

  • Path to bus file

Params

  • extra: Optional parameters

Authors

Code

#!/usr/bin/env python3
# coding: utf-8

"""Snakemake wrapper for bustools sort"""

__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2022, Thibault Dayris"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"

from snakemake.shell import shell
from tempfile import TemporaryDirectory
from snakemake_wrapper_utils.snakemake import get_mem

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")

bus_files = snakemake.input
if isinstance(bus_files, list):
    bus_files = " ".join(bus_files)

mem = get_mem(snakemake, "MiB")


with TemporaryDirectory() as tempdir:
    shell(
        "bustools sort "
        "--memory {mem} "
        "--temp {tempdir} "
        "--threads {snakemake.threads} "
        "--output {snakemake.output[0]} "
        "{bus_files} "
        "{log}"
    )