RSEQC BAM_STAT.PY

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Summarizing mapping statistics of a BAM or SAM file.

URL: https://rseqc.sourceforge.net/#bam-stat-py

Example

This wrapper can be used in the following way:

rule test_rseqc_bam_stat:
    input:
        "a.bam",
    output:
        "a.stats",
    threads: 1
    params:
        extra="--mapq 5",
    log:
        "bastat.log",
    wrapper:
        "v5.8.0/bio/rseqc/bam_stat"

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

Only mapping quality can be provided as optional parameters, since –help and –version do not produce summary.

Software dependencies

  • rseqc=5.0.4

Input/Output

Input:

  • Path to BAM/SAM file(s) to summarize.

Output:

  • Path to summary

Params

  • extra: Optional argument basides –input-file

Authors

  • Thibault Dayris

Code

# coding: utf-8

__author__ = "Thibault Dayris"
__mail__ = "thibault.dayris@gustaveroussy.fr"
__copyright__ = "Copyright 2024, Thibault Dayris"
__license__ = "MIT"

from snakemake import shell

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

shell("bam_stat.py --input-file {snakemake.input[0]} > {snakemake.output} {log}")