Use old snakemake wrappers with `nodefaults` instead of `defaults` in the yaml file

[gernophil]

Hey everyone,
I need to rerun some old workflows for new datasets. Due to the latest development all the anaconda channels are blocked globally on our HPC. These old wrappers still have the defaults channel in the yaml files and that's why environment creation fails for these.

I could of course update all the wrappers to the new versions, which now include the nodefaults channel, if I got that correct, but for reproducibility and compatibility reasons, I don’t want to change the workflow (and the version of the used tools) itself. The packages though should be available in their needed versions also on the nodefaults channels.

Is there an easy way how I could simply override the wrappers yaml file and still use that wrapper version? I could clone the whole repository and manually edit these and then call the wrappers from this repo, but maybe there is an easier way.

[fgvieira]

I think that if you supply a conda YAML file to the rule, that it will take precedence over the env on the wrapper. For example:

rule samtools_view:
    input:
        "{sample}.sam",
    output:
        bam="{sample}.bam",
        idx="{sample}.bai",
    log:
        "{sample}.log",
    conda:
        "/path/to/local/conda/env/samtools.yaml",
    threads: 2
    wrapper:
        "v5.2.0/bio/samtools/view"

This should use the wrapper from v5.2.0 but with the conda environment specified in conda. Of course, you'd have to make sure that the version specified in conda is compatible with the wrapper.

[gernophil]

Ah ,that's good to know. I just cloned the whole repo of the version I needed and changed every yaml file in there :D.

[fgvieira]

If you ever try providing a local conda YAML file, could you report back if it works or not? Thanks!

[gernophil]

I will :).