Steps

Steps are independently runnable pipeline units with declared configuration, inputs, outputs, and dependencies. Each reference page documents one step’s runtime contract.

Use asokai list -v steps to include internal steps. asokai describe step <name> shows their details when named explicitly; add -v for configuration keys, file details, and dependency trees.

Core steps

Core steps establish the shared data used by the rest of the pipeline:

• download-genome — Downloads genome DNA, cDNA, annotation, and a reusable annotation database.

• create-target-gene — Creates a target gene, extracts target sites, and writes a region FASTA.

• generate-therapeutic-candidates — Generates therapeutic candidates for target sites.

Analysis steps

Analysis steps calculate properties of pipeline data and write typed result tables. Built-in analysis steps are listed below. The Analyses index also includes tasks that compose an analysis from multiple steps.

• compute-intrinsic-features — Computes nucleotide composition and CpG features for each target site.

Utility steps

Utility steps perform reusable operations on supplied inputs. Run selections or tasks can connect them to specific ASOkai data sources.

• build-kmc-index — Builds a reusable KMC KFF index from a FASTA reference.

• build-bowtie2-index — Builds a Bowtie 2 index directory from a FASTA reference.