Addressing TODOs in pipeline, general cleanup of variables

[nschcolnicov]

Address the TODOs left in the pipeline.
Check variables, add "ch_" to channel and "val_" to value variables
Make sure that variable names remain consistent across workflows.
Assess which emitted files from subworkflows are actually being used.
Replace any dsl1 or groovy funcitons which can be replaced with nextflow DSL2 functions.

[nschcolnicov]

• Standardize ch_bowtie_index: standardize ch_bowtie_index channel structure #451
• Replace untarfiles with untar: Replace untarfiles with untar #449

[nschcolnicov]

All set