Snakemake wrappers fails to open environment file: HTTP Error 404: Not Found

Question

When using snakemake wrappers with snakemake version 5.5.2 like this:

rule bcf_to_vcf:
    input:
        "{prefix}.bcf"
    output:
        "{prefix}.vcf"
    params:
        ""  # optional parameters for bcftools view (except -o)
    wrapper:
        "0.38.1/bio/bcftools/view"

I get the following error:

Building DAG of jobs...
WorkflowError:
Failed to open environment file https://bitbucket.org/snakemake/snakemake-wrappers/raw/0.38.1/bio/bcftools/view/environment.yaml:
HTTPError: HTTP Error 404: Not Found

Apparently, the wrapper files are no longer available on bitbucket.

Answer 1

TL/DR:

To use snakemake-wrappers version 0.38.1 and above, you need to use snakemake version 5.7.0 or higher.

What is going on:

Snakemake (and snakemake-wrappers) recently migrated from bitbucket to Github. This causes some minor inconvenience with the paths to the snakemake-wrappers repository used internally by snakemake. The easiest way to solve this is to update snakemake to version 5.7.0 or newer. These version already use the new paths to the Github version.

While the bitbucket repo of snakemake wrappers is still online, it only contains the snakemake-wrapper versions 0.38.0 and lower. To use a higher version of snakemake-wrappers (as 0.38.1 in the code above), you need a newer version of snakemake, which pulls workflow data from the Github version of snakemake-wrappers repo.