Add to template module that records selected pipeline parameters.

[jfy133]

Suggestion

Generate a params.json file containing all selected parameters for a given run, and display this at the end of MultiQC report alongside software_versions.

Use Case/Rationale

Inspired by the tower.nf 'configuration' display, provides a 'hard' copy of the exact parameters used in a given run in the MultiQC report (which would be acommon calling-point for post-run validation).

e.g. could be useful if presenting a MultiQC report in a meeting, and a collegue asks what parameter you used for XYZ - if you can't remember exactly - you can then can scroll down to the bottom of the report to see).

Possible Implmentation

Can exploit: nextflow-io/nextflow#1682 (comment)

i.e.

log.info("workflow params")
log.info("${params}")

to be parsed into a custom MultiQC params.json or TSV file, that is also added to the MultiQC config.

Notes from @ewels:

(same as how we do it with the launch tool)
But fine to put in MultiQC if it’s a table that becomes scrollable automatically when long I guess or something

[jfy133]

Originally idea was to display in MultiQC, but might be worth keeping this optional.

However, could still export a JSON/TSV file with the parameters to pipeline_results/, and leave it up to pipeline devs to export this for display in MultiQC

[jfy133]

nf-core/modules#1161

[ewels]

Suggested simple implementation for the @nf-core template by @bentsherman here:

Well, we could simplify @stevekm 's example to a regular Groovy function, or use the workflow complete handler:

import groovy.json.JsonOutput

workflow.onComplete {
    jsonStr = JsonOutput.toJson(params)
    file("${params.outdir}/params.json").text = JsonOutput.prettyPrint(jsonStr)
}

Originally posted by @bentsherman in nextflow-io/nextflow#1515 (comment)

Suggest we put this into the template for all nf-core pipelines, as a default output for the pipeline_info directory.

'cc @JoseEspinosa