126 enhancement suggestion turn off cell type clustering if bulk tissue

[ejh243]

Description

This pull request will make the cell type clustering check optional. To achieve this I have merged the two QC reports into one, with the second one now an optional chunk based on the ctCheck variable in the R config file. Had to move some other code sections around and reorder the commands in the job submission script.

Issue ticket number

This pull request is to address issue: #126.

Type of pull request

• [ ] Bug fix
• [X] New feature/enhancement
• [X] Code refactor
• [ ] Documentation update

Checklist

• [X] I have performed a self-review of my own code
• [X] I have commented my code, particularly in hard-to-understand areas
• [X] I have tested my code to check that it is functional
• [ ] I have used linters to check for common sources of errors
• [ ] I have implemented fail safes in my code to account for edge cases
• [ ] I have made the corresponding changes to the documentation

[ew367]

@ejh243 Has this code been tested on any of the devData datasets yet? Is there any example output for the new combined QC report anywhere?

[ejh243]

YEs I have tested it on my local copy of devData. I will send you the report output

[ejh243]

@ew367 all changes made and tested with both ctCheck = to TRUE and FALSE, can you re-review?