Hello all, I have a small question to put. In the CLI for ampliseq, putting samplesheet.csv is a mandate then why haven't you mentioned it in the "required" key? I see the --input parameter being added in the nextflow_schema.config for other pipelines like taxprofiler and so on but not for this one. I have attached the schema.json for ampliseq below:

Because only one of

--input

,

--input_fasta

, or

--input_folder

is required, see nf-co.re/ampliseq/2.18.0/docs/usage#… Would it be helpful to add that to the schema?

It would be helpful to have a required parameter for the input but I do understand that this is a typical OR case so, fixating on one of the many would be wrong.

I assume it would be correct to add

"oneOf": [
    {
        "required": ["input"]
    },
    {
        "required": ["input_fasta"]
    },
    {
        "required": ["input_folder"]
    }

to the schema. But thats not helping your case, is it? Is the documentation as linked above unclear? I am not certain what the issue exactly is and I am therefore not sure how to address it 😉

@Daniel Straub can you add a dependentRequired parameter for --skip_cutadapt when primers are omitted?

May I ask what you are aiming to achieve? Because that checks are in github.com/nf-core/ampliseq/blob/…/main.nf#… & github.com/nf-core/ampliseq/blob/…/main.nf#…

We are trying to build a platform around your pipeline. And I am supposed to write code in such a way that the nfcore's pipeline's version and the respective Nextflow's version get mapped automatically while maintaining all the required and default parameters of the pipeline. In order to achieve this I might need the "required: " key in your schema.json but unfortunately this isn't available for ampliseq's input parameters (coz of the OR condition). Thus, I asked if you can put them in the schema.json. I hope I am able to put myself well for you to understand

I see, yes, I understand. You are welcome to open issues/PRs to adapt the pipeline as needed.