Add Cutadapt to Alignment Workflows

Cutadapt Added to Alignment Workflows

This release adds Cutadapt functionality to the BWA/GATK and Sentieon Alignment Workflows. The Cutadapt features are controlled using the cutadapt_r1_adapter and cutadapt_r2_adapter inputs (see the workflow docs for details on other inputs for tuning Cutadapt). Providing only the former for SE reads and both for PE reads will activate Cutadapt. The workflow will provide the stats from the Cutadapt runs as an output.

Docker Tables

Also, in the docs directory, this release adds tables describing the Dockers present in each of our production public apps. These tables are a quick and easy way to see the various tools and dockers present in these workflows.

What's Changed

• ✂️ add cutadapt by @dmiller15 in #132
• 🤖 add docker table builder gha by @dmiller15 in #133

Full Changelog: v2.9.1...v2.10.0