Open ChrOertlin opened 5 months ago
I think for the upcoming technologies makes sense to do ONT
samplesheet
and illumina
samplesheet
, but I think the workflow sample sheet is completely different from the sequencing sample sheet. It is just unfortunate that they have the same name. I think that putting the sequencing sample sheet and the workflow sample sheet under the same tag will mix up irreversibly these two file types.
I would argue that they while their purpose are different, both the samplesheet of the flow cells as well as the workflows are samplesheets. It is just a file that contains samples and sample metadata that is consumed in one way or another.
If we use StrEnum and go for many tags we can do:
class Prerequisite (StrEnum)
CONFIG = auto()
SAMPLESHEET = auto()
which is more MERRy (Maintainable, Extendable, Readable and Robust) and pythonic.
Description
A question on slack brought up a discussion on usage of tags in housekeeper.
The question was whether to add
samplesheet
as a tag for samplesheets used in workflows. However, curretnylsamplesheet
is "reserved" or "limited to"flow-cell
samplesheets. Currently the solution is to add a new tag using:nextflow-samplesheet
.Basically we are creating a new tag consisting of two tags, which to me seems counterintuitive. Ideally these should be two tags.
nextflow
andsamplesheet
. Furthermore, this pattern oftag-tag
seems to exist for files likenextflow-config
.To do
Discuss the design patterns of tags, decide what to do, document and implement decision.
Some other points brought up
Especially with upcoming new technologies in production that possibly also require
samplesheet
´s (pacbio
,ONT
,Sephyr
) and other files we likely need to introduce new tags and retrospectively alterillumina
tags.Example of inefficient tag usage / construction
The![image](https://github.com/Clinical-Genomics/housekeeper/assets/8860786/6ae7a8bf-aef5-4b6f-b83f-425db97ec0d6)
VariantTags
in hermes - althought here might be some additional step involved that I do not fully understand, yet.