Joining files in channel

[Chris D]

Suppose I have the following:

process A {

    input:

    some input

    output:

    some output in variants

    """

    freebayes -f ref.fa alignment.bam into variants

    """

}

Is there a way to take the files placed in the variants channel and do a join outside of the process and use the result for input into another process? For example,

def variant_files = variants.join(" ")

[Paolo Di Tommaso]

For join do you mean to collect all of the use in a single shot? 

If you ca use toList as shown here for example: 

https://github.com/nextflow-io/examples/blob/master/split_and_gather.nf#L63

Cheers,

p

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[Chris D]

Yeah, I want to collect all of the inputs in a single shot so I can use bcftools for multiple vcf intersection, but as far as I can tell bcftools needs the format to be:

bcftools -isec -p dir A.vcf B.vcf C.vcf

Can I use toList for this?

On Tuesday, October 4, 2016 at 11:04:40 AM UTC-6, Paolo Di Tommaso wrote:

For join do you mean to collect all of the use in a single shot? 

If you ca use toList as shown here for example: 

https://github.com/nextflow-io/examples/blob/master/split_and_gather.nf#L63

Cheers,

p

On Tue, Oct 4, 2016 at 6:58 PM, Chris D <cde...@rams.colostate.edu> wrote:

Suppose I have the following:

process A {

    input:

    some input

    output:

    some output in variants

    """

    freebayes -f ref.fa alignment.bam into variants

    """

}

Is there a way to take the files placed in the variants channel and do a join outside of the process and use the result for input into another process? For example,

def variant_files = variants.join(" ")

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[Paolo Di Tommaso]

Yes! 

p