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Robust Submission Inputs (Issue #81) #140

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merged 30 commits into from
Jan 30, 2024

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Description

Please Describe the Bug(s) Fixed and/or the Feature(s) Added:
Made the inputs into submission optional for certain databases.

Checklist

Go Through Checklist Below and Place A ✔️ (X Inside the Box) if Completed

General Checks

  • Have you run appropriate tests (unit/integration/end-to-end) to check logic across run environments (Conda/Docker/Singularity on Scicomp/AWS/NF Tower/Local)?

    For each relevant configuration:

    • Can the program run completely through without erroring out?
    • Does it produce the expected outputs, given the inputs provided?
  • Have you conducted proper linting procedures?

    • Numpy formatted docstrings for functions
    • Comments explaining lines of code
    • Consistent and intuitive naming conventions for variables, functions, classes, methods, attributes, and scripts
    • Single empty line between class functions, two lines between non-class functions, and two lines between imports and code body
    • Camel case formatting for class names
  • Have you updated existing documentation (README.md, etc.) or created new ones within docs?

CDC Checks

  • Did you check for sensitive data, and remove any?
  • If you added or modified HTML, did you check that it was 508 compliant?

Are additional approvals needed for this change? If so, please mention them below:
N/A

Are there potential vulnerabilities or licensing issues with any new dependencies introduced? If so, please mention them below:
N/A

…ing + stops program if necessary files are missing
…thin this script but inside of general_utility.py instead
…iles + fixed parameter checks to remove sections that require certain paths to exist for files
…likely to change + removed the need for params.variola and just using --organism flag now + nextflow.config has many updated default params
@ankushkgupta2 ankushkgupta2 self-assigned this Jan 30, 2024
@ankushkgupta2 ankushkgupta2 merged commit 85b2420 into dev Jan 30, 2024
@ankushkgupta2 ankushkgupta2 deleted the 81-internal-robust-submission-inputs branch January 30, 2024 20:19
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