Copy the contents of a directory to an output directory.

Meant to be combined with a publishDir directive at the call site: the
run-specific part of the destination travels through --output (which the
caller builds from the state), while the publish root is supplied by the
publishDir directive.

Save a base64-encoded run state to a YAML file for reproducibility.

Bulk RNA-seq pipeline: FastQC (raw + trimmed) → TrimGalore → Kallisto pseudo-alignment
(preliminary quantification) running in parallel with STAR alignment → Salmon
quantification (alignment mode) + Qualimap coordinate-based QC → MultiQC.

Opinionated runner for the bulk RNA-seq pipeline.