publish-process-outputs.nf

#!/usr/bin/env nextflow

/*
 * Copyright (c) 2018, Centre for Genomic Regulation (CRG).
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 * 
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 * SOFTWARE.
 */

 /*
  * author Paolo Di Tommaso <paolo.ditommaso@gmail.com> 
  */

params.reads = "$baseDir/data/reads/*{1,2}.fq.gz"
params.outdir = 'my-results'

Channel.fromFilePairs(params.reads, checkIfExists: true).set{ samples_ch }  

process foo {
  publishDir "$params.outdir/$sampleId"
  input:
  set sampleId, file(samples) from samples_ch
  output:
  file '*.fq'

  script:
  """
  < ${samples[0]} zcat > sample_1.fq 
  < ${samples[1]} zcat > sample_2.fq 
  """
}