search

nf-core / methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
https://nf-co.re/methylseq
MIT License
137 stars 136 forks source link

Add bwameth test config #364

Closed scoughlan2 closed 8 months ago

scoughlan2 commented 8 months ago

Description of feature

test and test_full configs only test the bismark workflow but not the bwameth subworkflow which means that breaking changes to that workflow can potentially go unnoticed. I am proposing adding a separate test config for the bwameth subworkflow to ensure that it can also be easily tested.

sateeshperi commented 8 months ago

Hello, I wanted to point out that we do in fact nf-test for all the three different aligners: bowtie2(default) hisat2 bwameth

you can run any of these tests by their tags as nf-test test --tag bwameth --profile docker

The github CI is designed to run all these tests upon changes and verifies against previously recorded snapshot containing the md5sum of files and existence checks.

As it is there is no need for a different test config as the aligner can be specified via the CLI

Let me know if this addresses your concern for any changes to the bwameth workflow going un-noticed.

scoughlan2 commented 8 months ago

Thank you for explaining this. Yes this does address my concerns!

scoughlan2 commented 8 months ago

Closing