Fix multiple components

[sainirmayi]

Description

• bbmap_bbsplit: Fix argument type of --build to file and add output argument --index.
• kallisto_index: Fix --threads option.
• kallisto_quant: Fix output argument type and add output log file.
• rsem_calculate_expression: Fix command and output files.
• sortmerna: Fix output arguments and update docker image.
• umi_tools_extract: Remove --umi_discard_reads option and fix --log2stderr argument.

Issue ticket number

Closes #xxxx

Checklist before requesting a review

• I have performed a self-review of my code

• Conforms to the Contributing guidelines

• Proposed changes are described in the CHANGELOG.md

• I have tested my code with viash ns test --parallel -q <name or namespace>

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Documentation
  • Bug fixes

[rcannood]

Thanks for making all of these fixes! Some minor questions 😊

Could you add entries to the changelog for all of the components that were fixed?