A guide for developers of common implementation patterns

[mahesh-panchal]

Is your feature request related to a problem? Please describe.

It would be good to have a place to describe implementation patterns to common issues encountered by developers.

Describe the solution you'd like

A page with the implementation patterns that's easy to look up.

Additional context

Going through some code reviews, some common implementation issues pop up, that are sometimes addressed in strange ways. It would be nice to provide some best practice ways to deal with certain scenarios.

Examples:

• How to implement collectFile with meta information.

      Channel.of( [ id: 'test', taxid: 1234 ] )
          .tap { ch_data }
          .collectFile( newLine: true ) { meta -> [ "${meta.id}.tsv", "$meta.taxid" ] }
          .map{ file -> [ file.baseName , file ] }
          .join( ch_data.map { meta -> [ meta.id, meta ] }, by: 0 )
          .map{ id, idfile, meta -> [ meta, idfile ] }

• How should database's be handled for future use. Separate the database download and use storeDir instead of publishDir.
• How should one map to multiple databases/references. Use combine to make a Cartesian product of inputs vs indexes, and map and + to merge metadata appropriately.

[mahesh-panchal]

Throw an error on a empty channel:

params.something = 'test'
workflow {
    ch_in = Channel.empty()
        .ifEmpty{ error "Error" }
        .filter{ it != null }
    TASK( ch_in ).view()
}

process TASK{
    input:
    val message

    script:
    """
    echo $message
    """

    output:
    stdout
}

https://nextflow.slack.com/archives/C02T98A23U7/p1699950368556629?thread_ts=1699894501.983129&cid=C02T98A23U7

[mahesh-panchal]

How to use a function or closure to group channel operations