🛠️ Update to Add Extra Args and Docs

[migbro]

Description

Related to https://d3b.atlassian.net/browse/BIXU-3753 and https://d3b.atlassian.net/browse/BIXU-3760
A task failed as described in the second ticket. I've added a catch-most extra_args field to allow Ops to make adjustments as needed. Below are logs from a test run in which, after adjusting the recommended param, STAR was able to progress to 2nd pass mapping.

2024-09-16T17:58:49.745222942Z: STAR version: 2.7.10b compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source 2024-09-16T17:58:49.745226300Z: Sep 16 17:58:48 ..... started STAR run 2024-09-16T17:58:49.745228334Z: Sep 16 17:58:49 ..... loading genome 2024-09-16T18:00:50.483406675Z: Sep 16 18:00:50 ..... started 1st pass mapping 2024-09-16T18:32:58.819039457Z: Sep 16 18:32:58 ..... finished 1st pass mapping 2024-09-16T18:33:00.752898811Z: Sep 16 18:33:00 ..... inserting junctions into the genome indices 2024-09-16T18:37:23.221549264Z: Sep 16 18:37:23 ..... started mapping 

Sep 16 18:31:54   2229.4  1154329520       72    81.7%     77.1     0.3%     5.2%     0.5%     0.0%    11.8%     0.8%

Sep 16 18:32:54   2233.8  1193837461       73    82.0%     77.1     0.3%     5.2%     0.5%     0.0%    11.5%     0.8%

Sep 16 18:32:58	Finished 1st pass mapping

Sep 16 18:38:23   1764.6    29409190       77    88.1%     77.1     0.3%     6.4%     0.6%     0.0%     4.0%     0.9%

Sep 16 18:39:23   1864.8    62159655       77    88.2%     77.1     0.3%     6.4%     0.6%     0.0%     4.0%     0.9%

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

• Test task. Was aborted as this will be run in the harmonization project fully. Test task demonstrates fix should work.
• Test B

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