Snakemake bug when mainWorkflowURL is github repo

[KevinSayers]

Describe the Bug

A github repo can't be used as the mainWorkflowURL currently with the Snakemake engine.

Steps to Reproduce Include a repository as the mainWorkflowURL

{
  "mainWorkflowURL": "https://github.com/KevinSayers/AWS_POC_Snakemake.git",
  "inputFileURLs": [
    "inputs.json"
  ],
  "engineOptions": "-j 5 --use-conda --printshellcmds"
}

Relevant Logs

== Finding the project in  ==
--
cd https://github.com/KevinSayers/AWS_POC_Snakemake.git
/opt/bin/snakemake.aws.sh: line 144: cd: https://github.com/KevinSayers/AWS_POC_Snakemake.git: No such file or directory

Expected Behavior

AGC should pull the workflow and then cd into the directory.

Actual Behavior

AGC tries to cd into the url.

Screenshots

Additional Context Other workflow engines such as Nextflow can pull repos directly if provided a repo URL. Snakemake doesn't have this functionality so I think the bash script needs to be modified to first pull the repo then cd. Changes may be needed around here: https://github.com/aws/amazon-genomics-cli/blob/main/packages/engines/snakemake/snakemake.aws.sh#L127

Operating System: AGC Version: 1.5.0 Was AGC setup with a custom bucket: No Was AGC setup with a custom VPC: No