process-per-file-pairs-custom.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 Matthieu Foll <follm@iarc.fr> 
  */

process foo {
  debug true
  tag "$sampleId"
  
  input:
  tuple val(sampleId), path(bam)

  script:
  """
  echo your_command --sample ${sampleId} --bam ${sampleId}.bam
  """
}

workflow {
  Channel.fromFilePairs("$baseDir/data/alignment/*.{bam,bai}", checkIfExists:true) { file -> file.name.replaceAll(/.bam|.bai$/,'') } \
    | foo
}