🤖 automate strand detection

[dmiller15]

Description

• Adds a tool developed by @zoomzoom1011 to automate the detection of strandedness.
• User no longer required to provide wf_strand_param input
• User provided wf_strand_param inputs will override detected strandedness.

Fixes # (issue)

Type of change

• [x] New feature (non-breaking change which adds functionality)

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

• [x] Single end test: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/80d35c58-88ff-4261-8365-f9d850cb29df
• [x] Paired end test: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/1108297e-c911-42fa-ae1d-f00f81b5577e

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

[dmiller15]

Do you think it's helpful/worth it to add as an output string the detected strandedness? So, to the wf, add an output detected_strandedness and just put the string value that is passed to wf_strand_param?

It would save a few seconds. Because you can just go to the output.json for the bam_strandedness step. I'm hesitant to add a new output right now as it would impact the flow for OPs (they'll be getting a new output). Perhaps when we refresh the workflow we could consider string outputs to use for debugging.