🔨 Modify Outputs

[migbro]

Description

RDS files are generally undesirable as they are sensitive to R versions and can be a bit bloated. Critical info has been broken out into TSV and h5 format files:

• QC metrics no longer buries in seurat object pulling them out into a simple TSV file
• Typical counts matrix store in h5 format instead, which can easily be converted into Cell Ranger style directories using DropletUtils and read in directly using popular Single Cell analysis software suite Seurat using Read10X_h5
• Updated docs to reflect these changes and prep for prod release

Fixes # (issue)

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

• QC only
• Within workflow - note, minor difference that table header names are different, before change implemented

Test Configuration:

• Environment:
• Test files:

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules
• I have checked my code and corrected any misspellings
• I have committed any related changes to the PR

[dmiller15]

What's up with the salmon-rnaseq submodule? Should that be here?