🎉 RNAseq Workflow V4 Pre-release party

[migbro]

Description

This builds on the STAR align and individual tool development work to create a complete workflow. The focus is mostly on establishing that workflow works and is robust, with a follow up to prep for an official release after review.

Fixes # https://github.com/d3b-center/bixu-tracker/issues/1317

Type of change

Please delete options that are not relevant.

• [ ] Bug fix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [x] 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

• [ ] BAM input
• [ ] FASTQ input

Test Configuration:

• Environment:
• Test files:

Checklist:

• [x] My code follows the style guidelines of this project
• [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 made corresponding changes to the documentation
• [x] My changes generate no new warnings
• [x] I have added tests that prove my fix is effective or that my feature works
• [x] New and existing unit tests pass locally with my changes
• [x] Any dependent changes have been merged and published in downstream modules
• [x] I have checked my code and corrected any misspellings
• [x] I have committed any related changes to the PR

[migbro]

Just a quick update - refactored bam2fastq and fastq steps to better reflect migration to cwl v1.2 bam2fastq update test: https://cavatica.sbgenomics.com/u/kids-first-drc/kids-first-drc-rnaseq-workflow/tasks/a9c6e92d-3bf0-4fda-b36f-58e6892ddab8/ cutadapt test: https://cavatica.sbgenomics.com/u/kids-first-drc/kids-first-drc-rnaseq-workflow/tasks/0bfc66ec-bfea-4702-a2a8-d4048ae24b20/

Even though task failed due to an unrelated downstream memory issue (technically I will have trimmed twice since reads were already trimmed), the tool implementation within the workflow is a success. PR https://github.com/d3b-center/bixtools/pull/133 needs to be merged first before this workflow will work properly.