Use JSON for meta data about modules HOT 4 CLOSED

I thought JSON is a bit out-of-fashion nowadays in favor of YAML/TOML as it's harder to read/write for human beings.

Is there no way of simplifying the config file instead? For instance, why can't this

input:
    -
        - input:
            type: file
            description: Input BAM or CRAM file
            pattern: *.{bam,cram}

just be that?

input:
        - input:
            type: file
            description: Input BAM or CRAM file
            pattern: *.{bam,cram}

(or in TOML)

[input]
  [input]
  type="file"
  description="Input BAM"
  pattern="*.{bam,cream"

from modules.

There was a reason.. Off the top of my head I think it was because inputs can have more than one item - eg. sample name and input file. So needs to be a nested list.

I agree that YAML is easier to read for simple stuff, but my point with this issue is that if we need more complex structures then it gets really easy to mess up YAML. JSON tends to be more verbose and clear in this case I think.

from modules.

NB: Maybe it’s massive overkill to record the inputs and outputs in this file. I was just putting down everything I could think of. In which case, yeah maybe the (existing) YAML is fine / better.

from modules.

I think we have somewhat come to a consensus as to the format and content of this file (YAML) having voted on Slack recently to have a description, inputs, outputs and authors section.

from modules.