feat(New hiseqx validation functions)

[karlnyr]

This PR adds new functions in validation of hiseqx SampleSheet. Specifically, they check wether there are more than type of indexes present(i.e., single or dual indexes) as well as an implementation of a sanity length check on dual indexes

How to prepare for test:

• [x] ssh to hasta
• [x] install on stage: bash servers/resources/hasta.scilifelab.se/update-demux-stage.sh feat/hiseq-samplesheet-validation

How to test:

• [x] login to hasta
• [x] us
• [x] run demux sheet validate --application wgs on:
  • [x] samplesheet with dual indexes of variable length
  • [x] samplesheet with multiple types of indexes

Expected test outcome:

• [x] SampleSheets raises validation errors
• [x] Take a screenshot and attach or copy/paste the output.

Review:

• [ ] code approved by
• [x] tests executed by @karlnyr
• [ ] "Merge and deploy" approved by Thanks for filling in who performed the code review and the test!

This version is a:

• [ ] MAJOR - when you make incompatible API changes
• [x] MINOR - when you add functionality in a backwards compatible manner
• [ ] PATCH - when you make backwards compatible bug fixes or documentation/instructions

[henrikstranneheim]

@karlnyr What is the status of this one?

[karlnyr]

@karlnyr What is the status of this one?

I've written most of the tests already but got interrupted with production during Christmas. I Will most likely pick this up again next week 👍

[karlnyr]

I mixed up this PR and another one. I have now finished up the function and added a test for the function. The function is to be used in the demultiplexing workflow of hiseqx, so testing on hasta could be performed to test it.

[karlnyr]

Samplesheet with multiple index types:

Test:

Samplesheet with variable dual index length:

Test:

[karlnyr]

@barrystokman here it is

@henrikstranneheim only 5 months later after your first ping on the repo 👍

[karlnyr]

@barrystokman can you give me a review just to make it official? You may have already looked through the code but.... for appearance sake 💯

[barrystokman]

Let's decide what to do with the 2500 tests since I'm doing those in my PR as well.

[karlnyr]

@barrystokman I think I finally solved it all. After reverting, messing up merging 60+ times and pushing I think I finally managed to get the master into this branch. Can you please double check and then I will merge this and get on with the next PR

[henrikstranneheim]

Well done! 🎉