C
Concrete Hornet
We would like to build custom launch interfaces for nf-core pipelines in our Seqera Platform instance. By that I mean a restricted, minimal interface that only allows to set a minimal set of parameters while the rest is either frozen to a predefined default, or derived from these parameters.
For instance, for the nf-core/demultiplex pipeline, the only thing we'd like launch users to be able to set is the flowcell ID, the filename of the samplesheet and to which project this flowcell belongs. The input and output path shall be derived from the flowcell and project ID, and other options (e.g.
demultiplexer
) shall not be editable by the user. For instance, to derived the outdir from the
project_id
, we'd envisage something like
params.outdir = "s3://some-company-namespace-${params.project_id}/demultiplex"
.
To achieve this, for now, we built a custom Nextflow pipeline that wraps the nf-core pipeline with a custom schema. Example. However, ideally, the same could be achieved directly in Seqera Platform. For that, I believe the following would be necessary:
  • support for custom schemas outside the pipeline repo, see also
  • support for custom
    nextflow.config
    outside the pipeline repo
  • some sort of scripting to manipulate params and possibly input samplesheets (i.e. generate params and samplesheets from whatever is specified in the custom schema).