Ideas for configuration of pipeline execution

[rroutsong]

How do we inform our software on which snakemake pipelines to run, and which not to.

Currently this information is kept in the LabKey database in a free form text.

For these values to be useful they need to have a controlled vocabulary.

Here's a list of analysis types supported by openomics pipelines:

ATAC-seq
Methyl-seq
ChIP-seq
RIP-seq
RNA-seq
miRNA-seq
WGS
WES
16S targeted sequencing
Viral metagenomics sequencing
Shotgun metagenomics sequencing
single-cell ATAC-seq
single-cell RNA-seq

By default the RNA-seq pipeline should be ran

[rroutsong]

Example of a labkey requests table
EXAMPLE_REQUEST_TABLE.txt

[rroutsong]

Request type looks to be informative of which analyses to run. But need to discretize the database column before using.