ingest: Split monolith transform rule

[joverlee521]

Context

Currently in the ingest pipeline, there is a single transform rule that runs a shell pipeline of multiple Python scripts. This works in the automated ingest pipeline, but may be tedious to debug when developing or when there's an error in the pipeline.

Description

We can split up the single rule into multiple rules by using Snakemake's piped outputs feature. I don't think anyone in the group has used this feature, so we don't know the pitfalls.

[joverlee521]

I experimented with Snakemake's piped outputs feature in a small example workflow and it errors when you provide less cores than the number of connected piped outputs, which is not great.

The curate pipeline has since propagated to many other pathogen ingests and works well so I'm closing this as not planned.