Run two gastric samples for bulk RNA-seq

[cbethell]

Related to a bullet point from this comment on the potential bulk RNA-seq changes inspired by 2020 May and 2020 June trainings issue #240,

We should run two gastric samples for the bulk RNA-seq material since everyone is now similarly equipped using RStudio Server, and participants would typically have more than one sample that they want to process, thus giving them a better starting point.

Also from that bullet point, we should consider

using a Makefile instead of a bash script for this per advice someone gave @cgreene

Edit: We should consider using Snakemake instead of a bash script.

[cgreene]

Probably snakemake but I don't remember this 😂

[jaclyn-taroni]

A later comment on the issue being broken up was essentially "Josh said to use snakemake instead."

[cbethell]

A later comment on the issue being broken up was essentially "Josh said to use snakemake instead."

Ah yes:

Forgot to note that during some discussion @jashapiro thinks Snakemake in the absence of wildcards is easier to learn than Make

That comment appeared to be a bit lonesome to me at first glance and I forgot to take another whack at connecting it to its related point before closing that issue. Updating the original comment on this issue 👍