cnvkit batch wrapper fails if input file name contains extra delimiters

[andrewgull]

Snakemake version
v9.6.2

wrapper version v5.2.1

Describe the bug

The CNVkit batch Snakemake wrapper currently fails to correctly locate output files when the input BAM filename contains extra delimiters (e.g., periods) or complex tags before the final extension. This occurs because CNVkit determines its output base name by stripping the extension from the input, but the wrapper's logic does not account for the possibility of a more complex base name.

Logs

cnvkit_batch_wrapper_error.txt

Minimal example

# the wrapper will throw the error with this input file names
rule cnvkit_batch:
    input:
        bam=["mapped/a.haplotag.bam"],
        bai=["mapped/a.haplotag.bam.bai"],
        reference="ref/reference.cnn",
    output:
        antitarget_coverage="cnvkit/a.antitargetcoverage.cnn",
        bins="cnvkit/a.bintest.cns",
        regions="cnvkit/a.cnr",
        segments="cnvkit/a.cns",
        segments_called="cnvkit/a.call.cns",
        target_coverage="cnvkit/a.targetcoverage.cnn",
    log:
        "cnvkit/a.antitargetcoverage.cnn.log",
    params:
        method='hybrid',  # optional
        extra="",  # optional
    resources:
        mem_mb=1024,
    wrapper:
        "master/bio/cnvkit/batch"

Additional context
As far as I know, this bug doesn't affect rule cnvkit_batch_build_reference