Feature request: `samplesheetToMaps` function

[adamrtalbot]

Sometimes, it would be useful to parse a samplesheet and return a key-val pair instead of a list of tuples as is returned by samplesheetToList. We could add a samplesheetToMaps function which returns a list of key-val pairs.

name,language,greeting
adam,english,hello
geraldine,french,bonjour

samplesheetToList('greetings.csv')
[
    [ 'adam', 'english', 'hello' ],
    [ 'geraldine', 'french', 'bonjour' ]
]

samplesheetToMap('greetings.csv')
[
    [ name: 'adam', language: 'english', greeting: 'hello' ],
    [ name: 'geraldine', language: 'french', greeting: 'bonjour']
]

[prototaxites]

I would be really interested in a function for this.

You can currently work around this by specifying the meta field for each key, but there are some idiosyncracies - for example, you get [] instead of null for an unspecified field, even if that field should just be a string.

[nvnieuwk]

In the future I will add a samplesheetToRecords function which will do approximately the same thing, but with the built-in records coming in the next Nextflow release. I think such a function would make more sense from a Nextflow point of view. Let me know if you disagree :)

#196

[prototaxites]

That would be a nice alternative too, I think 👍

[awgymer]

I started down this path once and I no longer remember why I didn't implement this functionality (something I couldn't support easily but no memory what). If records can be created from maps (i.e. something like record.new(map)) then I think that it might be possible to have this functionality much much more simply and just leverage the type-casting of records built in to nextflow?

For a plain map you could instead hopefully use and anonymous or empty record type (with all the undefined fields just being propagated through to the record) and it would effectively function as a map? For a specific record type we could have something like samplesheetToRecords(samplesheet, RecordType). This would obviously only support a single record type per samplesheet until or unless Nextflow adds support for discriminated unions of record types.

[nvnieuwk]

Yes that's exactly my idea for samplesheetsToRecords I'll do a POC once we have an edge version with records