nextflow-io/nextflow

I have a question about using Nextflow channels vs Groovy x= file() syntax when working with files in Nextflow. From what I understand, if we have a params.input="$baseDir/test-data/sample.txt" (i.e. a single file)

Option 1) Using Groovy: data = file(params.input) produces an object of class sun.nio.fs.UnixPath

If you later want to use the file in a process, you can do:

process testA {

    input:
    file x from data

    output:
    file '*' into result_ch

    script:
    """
    program -options  blah blah $x 
    """
}

Option 2) Making a channel such as below also produces an object of class sun.nio.fs.UnixPath

Channel
    .fromPath(params.input)
    .set {data_ch}`

If you later want to use the file in a process, you can do:

process testA {

    input:
    file x from data_ch

    output:
    file '*' into result_ch

    script:
    """
   program -options  blah blah $x 
    """
}

So my question is: why chose one option over the over, if both options end up with Nextflow "understanding" you have a file object you want to use for a process? Should you not be making a Nextflow channel if you have a single file?

I feel I am missing something here. I know that using option 1) can be useful if you want to manipulate a file, a file name (or its path) later on in a process, prior to the script: string command:

process testB {

    input:
    tuple val(chromosome), val(sample), file("sample.bed") from channel_ch
    file(data)

    output:
    tuple val(chromosome), val(sample), file("sample.log")

    script:
    ref1 = file(data + ref_path.name +  "/" + sprintf(params.refHapFilesPattern, chromosome))

    """
    program -options  $samples.bed $ref1 \\
    """
}

I guess what I'm asking, more broadly is:

• Is there a general situation (s) where should you be using Groovy syntax rather than a Nextflow channel
• Is there a general situation where one should use Groovy variables prior to the """ part of the process "script:".

Thanks