✨ multi readgroup input

[dmiller15]

Description

This update brings multi-read group processing to RNAseq.

The workflow can now handle multiple inputs in the form of lists:

• input_aligned_reads
• input_pe_reads
• input_pe_mates
• input_se_reads

Aligned reads inputs have their @RG headers pulled and used for processing. Otherwise read groups inputs are also provided in list format using:

• input_pe_rg_strs
• input_se_rg_strs

These lists are converted to a record schema I have defined externally and import throughout the workflow. STAR and Kallisto had their inputs updated to take this record input to assist in building the command line.

This approach mirrors what we have in the DNAseq alignment workflows. Many of the new tools are stolen directly from the alignment workflow repo.

Closes https://d3b.atlassian.net/browse/BIXU-3780

Type of change

• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• 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

• Multi-RG BAM input: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/89142fa5-e64b-4dad-8d11-acf05e184381
• Multi-RG PE FASTQ input: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/ecb59f16-758c-4a3d-9acb-522b684e8961

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

[migbro]

What a behemoth! Impressive work. Just a couple minor typos I saw, but no obvious flaws in logic that I could see