Allow fromFilePairs to handle non globbing file patterns

[ODiogoSilva]

A common pattern to support having both single or paired-end reads onto the same channel definition is to do something like:

Channel.fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )

This works fine for when params.reads is a glob pattern, but if you provide only a single file with an absolute path like:

--singleEnd --reads "/absolute/path/to/single/fastq.gz"

Nextflow throws an error:

ERROR ~ No signature of method: nextflow.Channel$_fromFilePairs0_closure6.call() is applicable for argument types: (sun.nio.fs.UnixPath) values: [/home/diogo/test/teste1]
Possible solutions: any(), any(), any(groovy.lang.Closure), each(groovy.lang.Closure), tap(groovy.lang.Closure), any(groovy.lang.Closure)

 -- Check '.nextflow.log' file for details

An immediate solution would be to add a wildcard to the provided path, but would it be possible for the fromFilePairs channel to also accept UnixPath arguments?

[pditommaso]

Not sure why this is happening. I think the main reason is that it's not founding the any wildcard character.

[maxibor]

Same issue here.
NF channel code:

Channel
    .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
    .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\n" }
    .into { reads_to_trim; reads_fastqc }

Params file

params {
    singleEnd = true
    reads = "/path/to/singleEnd.fq"
}

Yields:

Launching `main.nf` [high_northcutt] - revision: bcb793296b
true
class java.lang.Boolean
ERROR ~ No signature of method: nextflow.Channel$_fromFilePairs0_closure6.call() is applicable for argument types: (sun.nio.fs.UnixPath) values: [/path/to/singleEnd.fq]
Possible solutions: any(), any(), each(groovy.lang.Closure), any(groovy.lang.Closure), each(groovy.lang.Closure), any(groovy.lang.Closure)

 -- Check '.nextflow.log' file for details
ERROR ~ Cannot find any reads matching: /path/to/singleEnd.fq

However, if I set the params to the following, it works:

params {
    singleEnd = true
    reads = "/path/to/singleEnd.*"
}

Nextflow version: nextflow version 0.31.1.4886
Java version: openjdk version "1.8.0_152-release"
System version: Ubuntu 14.04.5 LTS

[pditommaso]

This commit implements the support for non globbing pattern for
Channel.fromFilePairs method. This means that it is possible to
specify a file path without any wildcard as matching pattern, eg.

Channel.fromFilePairs('/some/path/file-name.txt') 

It returns the pair:

['file-name', ['/some/path/file-name.txt']]

Bonus: when the specified pattern does not contain any wildcard
character it defaults automatically to single pair, therefore
it’s not necessary to specify size: 1 to handle this scenario.