DSL2: Pre-Release Checklist

This is the list of pending tasks for eager 3.0.0 pre-release. If you see can think of something more, please comment/add it below.

• Some modules (I noticed some metagenomics ones, but could be others too), are configured twice in modules.conf. Remove unnecessary configurations. #1173
• Ensure modules configuration blocks adhere to conventions in dev docs
• Merge #1169
• Merge #1168
• Update all modules to use topics (see #1170).
• Plug all MultiQC outputs into the actual MultiQC process.
• Update README.md.
• Remove any remaining dump() calls.
• Update usage.md:
  • This is mostly template, but would still need some tweaks to properly describe our pipeline. Below are some I noticed already:
  • Update samplesheet input and samplesheet fasta sections with all new params.
  • Add table with different samplesheet input columns.
• Update output.md:
  • We need to check that all sections have been documented. We've been pretty good with this at first, but we might have missed some as we go.
  • Sections need updating to data/ and stats/ subdivisions.
• Update the metro map!
• Nextflow strict syntax #1171

This checklist spans modules.conf, README.md, usage.md, output.md, the development code conventions, MultiQC outputs, and the metro map. Start by selecting one unchecked task and reviewing its referenced issue, such as #1173 or #1170. Done means every checklist item is completed and the pipeline is ready for the 3.0.0 pre-release.