A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Is it possible to use a params value as a default in a samplesheet?
• If provided, use `value`
• If not, `params.value`
• Extension: can we make `value` dependent on another field, e.g. `sample_type = "tumour"` changes the default value for`type` to `somatic` 

Nope these are not possible via JSON schemas, you can however easily implement these into your pipeline code :stuck_out_tongue:

The `default` implementation is pretty simple and just picks the first one it can find for that field. JSON schemas are super complex to code something with so it's in 99% of the cases just easier to implement it in the pipeline itself :stuck_out_tongue:

yup, that's how I've done it before and I'll do it again