Wrapper download fails due to incorrect GitHub path: mismatch between requested and actual wrapper URL

[bol7asan]

Snakemake version
9.3.3

Describe the bug
Snakemake fails to download a wrapper environment due to a mismatch between the path it attempts to fetch from and the actual structure of the wrapper repository on GitHub. Specifically, it tries to access:

https://github.com/snakemake/snakemake-wrappers/raw/v5.5.2/bio/deeptools/bamcoverage/environment.yaml

This results in a download error because that specific path/version combination does not exist or is invalid. This is not due to an outdated wrapper version, but rather an incorrect URL being constructed during wrapper resolution.

Logs

Creating conda environment https://github.com/snakemake/snakemake-wrappers/raw/v5.5.2/bio/deeptools/bamcoverage/environment.yaml...
Using pinnings from https://github.com/snakemake/snakemake-wrappers/raw/v5.5.2/bio/deeptools/bamcoverage/environment.linux-64.pin.txt...

Minimal example

rule bamcoverage:
    input:
        "mapped/{sample}.bam"
    output:
        "coverage/{sample}.bigwig"
    params:
        extra=""
    threads: 4
    wrapper:
        "0.87.0/bio/deeptools/bamcoverage"

Additional context
The wrapper system appears to hardcode or default to using the v5.5.2 version of the Snakemake wrappers repository even when a different version (like 0.87.0) is specified. This results in 404 errors or incorrect environment resolution. It would be helpful to either:

• Dynamically resolve the correct wrapper version path based on the user-specified wrapper version.
• Allow users to configure or override the wrapper repository version globally to avoid path mismatches.

[fgvieira]

That wrapper does not exits on v0.87.0 (it was first added on v1.30.0). Can you try with a more recent version (e.g. v6.2.0)?

[github-actions]

This issue was marked as stale because it has been open for 6 months with no activity.