DSL2: Pre-Release Checklist

[TCLamnidis]

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. DSL2: Duplicate module configurations in modules.conf #1173
• Merge DSL2: Bam deduplication without jobsplit #1169
• Merge DSL2: MultiVCFAnalyser #1168
• Update all modules to use topics (see DSL2: Update modules to use version topics #1170).
• Plug all MultiQC outputs into the actual MultiQC process.
• Update README.md.
• 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 Fix strict syntax errors #1171