Add option "checkIfExists" to Channel.fromPath method

[ewels]

It would be great if the .fromPath() channel generator could have a new option checkIfExists which, well, checks if it exists. Working with full file paths as well as globs.

See https://gitter.im/nextflow-io/nextflow?at=5ae0a290b01085166cbdb928 for discussion.

Phil

[ewels]

[pditommaso]

SUPER-LOL 😂😂😂

[stevekm]

might also be able to do a custom filter step for this?

[pditommaso]

What do you mean for custom filter step?

[stevekm]

Like this:

Channel.from([
    ['bad1', file('input/bad1.vcf')],
    ['good1', file('input/good1.vcf')],
    ['foo', file('input/foo.vcf')]
    ])
    .filter { sampleID, sample_vcf ->
        def file_exists = sample_vcf.exists()
        if (! file_exists) println ">>> WARNING: File ${sample_vcf} does not exist and will not be included"
        file_exists
    }
    .set { demo_exists }

[pditommaso]

It looks the above comment is off-topic.

[pditommaso]

Implementing this evil feature :)

I was just thuinking the checkIfExists is a bit verbose, what about shoudExist or mustExist, something else ?

[pditommaso]

OK, I went for checkIfExists that's the most redable. Available for test with version 0.32.0u2-SNAPSHOT.