These are chat archives for nextflow-io/nextflow

3rd
Feb 2017
Trevor Tanner
@tantrev
Feb 03 2017 03:07
Is there any way to get a channel from "groupBy()" ? I've tried using Channel.from() with it but it doesn't seem to work
Trevor Tanner
@tantrev
Feb 03 2017 03:19
nvm, figured it out! should've known another flatMap() would do the trick
Manuel
@kohleman
Feb 03 2017 14:49

I got a very simple question. How can I use the read_pairs variable in the code below such that I use only a part of this string?
Everything failed when I tried to change this variable.

Channel.fromFilePairs(params.reads)
                .ifEmpty { error "Cannot find any reads matching: ${params.reads}" }
                .set { read_pairs }

process trim {

    tag "${pair_id}"

    publishDir "${params.outpath}/${params.title}/$pair_id".tokenize('_')[2], mode: 'link'

[..]
}

ERROR ~ No such variable: pair_id

-- Check script 'trimmomatic.nf' at line: 31 or see '.nextflow.log' file for more details