`agc workflow run` always zips everything

[multimeric]

Describe the Bug

agc workflow run will zip whatever is at the sourceURL of the workflow in question, even if it is:

• A single file ie main.nf
• Already a zip file, ie bundle.zip, which contradicts the documentation

Steps to Reproduce

• Have the following agc-project.yml:

  name: SomeWorkflows
  schemaVersion: 1
  workflows:
  somePipe:
  type:
    language: nextflow
    version: 1.0
  sourceURL: bundle.zip
  contexts:
  SomeContext:
  instanceTypes:
    - "c6g.medium"
  engines:
    - type: nextflow
      engine: nextflow

• agc workflow run somePipe --context SomeContext

• Grab the S3 URL of the archive from the AWS Batch console Job page
• Download the file from S3
• Unzip it
• You will notice that inside workflow.zip is bundle.zip, which is not correct behaviour

Relevant Logs

n/a

Expected Behavior

workflow.zip should be bundle.zip, not contain it. So for example main.nf should be a file in both.

Actual Behavior

workflow.zip contains bundle.zip

Screenshots

n/a

Additional Context

Operating System: AGC Version: 1.1.2 Was AGC setup with a custom bucket: No Was AGC setup with a custom VPC: No

[github-actions[bot]]

Greetings! Sorry to say but this is a very old issue that is probably not getting as much attention as it deserves. We encourage you to check if this is still an issue in the latest release and if you find that this is still a problem, please feel free to open a new one.

[waliag87]

Hello @multimeric we have reopened the ticket and will work to fix this as soon as possible

[github-actions[bot]]

Greetings! Sorry to say but this is a very old issue that is probably not getting as much attention as it deserves. We encourage you to check if this is still an issue in the latest release and if you find that this is still a problem, please feel free to open a new one.