adding bed file input

[jrotieno]

Closes #189

🛠️ Changes Being Made

Added an optional snippy_core_bed file input to the Snippy_Tree workflow, and thereby exposing this optional input to the Snippy_Streamline workflow

🧠 Context and Rationale

Whereas a bed file optional input can be used to mask an alignment in Snippy_Tree, this input is not exposed as an option in Snippy_Streamline. This limits ability to use Snippy_Streamline for TB phylogenetics that needs masking of certain repeat regions.

📋 Workflow/Task Steps

Inputs

the added optional input snippy_core_bed

Outputs

Remain the same

🧪 Testing

Locally

Input exposed locally

Terra

Input exposed on Terra

🔬 Quality checks

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The workflow/task has been tested locally and on Terra
• The CI/CD has been adjusted and tests are passing
• Everything follows the style guide

[emmadoughty]

Code looks good!

Tested on Terra: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Doughty_Sandbox/job_history/72c20877-46e5-48a1-8b28-7a8dc40d06e8

Confirmed that output is exposed in Snippy_Streamline workflow and bed file is being used to mask the alignment.

Great work getting this sorted!