Tools: Remove `params.singleEnd` from the expected parameters during linting

Created on 19 Sep 2019 · 3Comments · Source: nf-core/tools

Hi all,

feedback from the nf-core hands-on session from @aunderwo (thanks!).

nf-core lint raises a warning, if the params.singleEnd is not set in the pipeline. I think we can remove this requirement from the hardcoded list of parameters, as this is strongly bound to the NGS domain and should not be a basic nf-core required parameter.

https://github.com/nf-core/tools/blob/c34b04bf8039de39c3fd8a41a75cdaf2dbfc90ae/nf_core/lint.py#L354

Any thoughts?

best, Sven

Source

sven1103

Most helpful comment

Yeah, we should probably make these more general. If we switch to --input then we should add a test to make sure that pipelines _don't_ have --reads any more, so that all are consistent.

Phil

ewels on 23 Sep 2019

👍3

All 3 comments

I'm all for it, I would also add --input as an alternative for --reads

MaxUlysse on 19 Sep 2019

👍1

Yeah, we should probably make these more general. If we switch to --input then we should add a test to make sure that pipelines _don't_ have --reads any more, so that all are consistent.

Phil

ewels on 23 Sep 2019

👍3

Fixed in https://github.com/nf-core/tools/pull/556