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Dev #153

Merged
merged 329 commits into from
Feb 2, 2024
Merged

Dev #153

merged 329 commits into from
Feb 2, 2024

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kyleoconnell
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Description

Please Describe the Bug(s) Fixed and/or the Feature(s) Added:

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:

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

kyleoconnell and others added 30 commits December 15, 2023 15:51
…n_workflow + uncommented the signal input within the metadata_validation process to align inputs from main_workflow to the inputs in the process for metadata_validation
…ption for the annotation tools for only pre-split FASTA files + changed the fasta file parameter description to single samples
…recipients during a table2asn genbank submission
ankushkgupta2 and others added 24 commits January 29, 2024 13:33
…likely to change + removed the need for params.variola and just using --organism flag now + nextflow.config has many updated default params
…ain default values that need to be populated when toggling between test profiles
@kyleoconnell kyleoconnell self-assigned this Feb 2, 2024
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@jessicarowell jessicarowell left a comment

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reviewed all files, made a minor comment correction, and deleted an old groovy file

@jessicarowell jessicarowell merged commit bb47dce into master Feb 2, 2024
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4 participants