SAMTOOLS COLLATE

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

Shuffles and groups reads together by their names.

URL: http://www.htslib.org/doc/samtools-collate.html

Example

This wrapper can be used in the following way:

rule samtools_collate:
    input:
        "mapped/{sample}.bam",
    output:
        "{sample}.collated.bam",
    log:
        "logs/{sample}.log",
    params:
        extra="-f",
    threads: 2
    wrapper:
        "v3.12.1-18-g9861c57/bio/samtools/collate"

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

  • samtools=1.20

  • snakemake-wrapper-utils=0.6.2

Input/Output

Input:

  • SAM/BAM/CRAM file

Output:

  • SAM/BAM/CRAM file

Params

  • extra: additional program arguments (not -@/–threads, –reference, -o or -O/–output-fmt).

Authors

  • Filipe G. Vieira

Code

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2024, Filipe G. Vieira"
__license__ = "MIT"


import tempfile
from pathlib import Path
from snakemake.shell import shell
from snakemake_wrapper_utils.samtools import get_samtools_opts


samtools_opts = get_samtools_opts(snakemake, parse_write_index=False)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

with tempfile.TemporaryDirectory() as tmpdir:
    tmp_prefix = Path(tmpdir) / "samtools_collate"

    shell(
        "samtools collate {samtools_opts} {extra} -T {tmp_prefix} {snakemake.input[0]} {log}"
    )