Incompatibility with certain non-alphanumeric characters will break workflow

markb729 commented 2 years ago

What happened?

When using a custom sample sheet, inclusion of certain non-alphanumeric characters will cause the pLannotate and report portions of the workflow to fail (e.g. a period "."). This looks to occur when the json.load function generates a dictionary automatically. Sample names that contain non-alphanumeric characters probably get filtered somewhere upstream, but the key is absent none-the-less and thus generates an error.

Operating System

ubuntu 20.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - Execution Profile

Docker

Workflow Version

d85691ac64

Relevant log output

Traceback (most recent call last):
    File "/home/.nextflow/assets/epi2me-labs/wf-clone-validation/bin/report.py", line 308, in <module>
      main()
    File "/home/.nextflow/assets/epi2me-labs/wf-clone-validation/bin/report.py", line 246, in main
      tup_dic = plannotate[item]
  KeyError: 'pL2029.1'

sarahjeeeze commented 2 years ago

Thanks for pointing this out, I will look in to this and get back to you.

sarahjeeeze commented 1 year ago

This was fixed in a more recent version of the workflow, Closing through lack of response from original poster.

epi2me-labs / wf-clone-validation