CODEWITHSUNDEEP
groovynextflow
aerijman
aerijman

Reputation: 2782

nextflow regex on path

The following works with strings:

Channel
.of('test1.fastq', 'test2.fastq', 'test1.bam', 'test2.bam')
.filter( ~/.*bam|.*1.fastq/ )
.view()

BUT not with paths. Is there a way to make this work with path? E.g.

Channel
.fromPath( params.inputs )
.filter( ~/.*bam|.*1.fastq/ )
.view()

Thankn you!

Upvotes: 3

Views: 691

Answers (1)

Steve
Steve

Reputation: 54502

The filter operator also lets you specify a closure, which would let you use Groovy's find operator, for example:

params.inputs = '*.{bam,fastq}'


workflow {

    Channel
        .fromPath( params.inputs )
        .filter { it.name =~ /(\.bam|1\.fastq)$/ }
        .view()
}

Another way to do what you want, I think, would be to use the find() method, which returns the first value in a list or null if no such element exists. Note that, according to the Groovy Truth, non-empty strings are coerced to true:

params.inputs = '*.{bam,fastq}'


workflow {

    Channel
        .fromPath( params.inputs )
        .filter { file ->
            ['.bam', '1.fastq'].find { file.name.endsWith(it) }
        }
        .view()
}

Upvotes: 3

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