Refactor trimming and filtering

[cjfields]

We are performing a few different variations of trimming and filtering, with many of these using mashups of cutadapt and DADA2's filterAndTrim.

• Illumina paired-end (non-variable, overlapping or non-overlapping) - only DADA2 filterAndTrim (16S V4, V3-V5)
• Illumina paired-end variable, overlapping + non-overlapping - cutadapt + DADA2 filterAndTrim (ITS)
• PacBio HiFi - cutadapt + filterAndTrim (full-length 16S)

It's worth setting these up as subworkflows based on the above choices; this would of course require DSL2.

[cjfields]

Addition of cutadapt for Illumina trimming and filtering is implemented in the cutadapt branch for DSL1 and should be easy to add for DSL2. This also includes code for adding read tracking, which is missing for any cutadapt steps (e.g., PacBio).