collect-and-merge.nf

#!/usr/bin/env nextflow
/*
 * Copyright 2013-2024, Seqera Labs
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */


/*
 * fake alignment step producing a BAM and BAI files
 */
process algn {
  debug true

  input:
  each barcode
  each seq_id

  output:
  tuple val(barcode), val(seq_id), file('bam'), file('bai')

  """
  echo BAM $seq_id - $barcode > bam
  echo BAI $seq_id - $barcode > bai

  """
}


/*
 * Finally merge the BAMs and BAIs with the same 'barcode'
 */
process merge {
  debug true

  input:
  tuple val(barcode), val(seq_id), file(bam: 'bam?'), file(bai: 'bai?')

  """
  echo barcode: $barcode
  echo seq_ids: $seq_id
  echo bam    : $bam
  echo bai    : $bai
  """

}

workflow {
  def ch1 = channel.of('alpha', 'gamma')
  def ch2 = channel.of('one', 'two', 'three')

  aggregation = algn(ch1, ch2)

  /*
   * aggregation is made by using a 'reduce' operator
   * followed by 'flatMap'
   */

   aggregation = algn.out
                     .reduce([:]) { map, tuple ->    // 'map' is used to collect all values; 'tuple' is the record containing four items: barcode, seqid, bam file and bai file
                         def barcode = tuple[0]      // the first item is the 'barcode'
                         def group = map[barcode]    // get the aggregation for current 'barcode'
                         if( !group ) group = [ barcode, [], [], [] ]    // if new, create a new entry
                         group[1] << tuple[1]        // append 'seq_id' to the aggregation list
                         group[2] << tuple[2]        // append 'bam' file to the aggregation list
                         group[3] << tuple[3]        // append 'bai' file to the aggregation list
                         map[barcode] = group        // set back into the map
                         return map                  // return it so that it will be used in the next iteration
                     }
                     .flatMap { it.values() }        // tricky part: get the list of values of in the map, each value is the
                                                     // aggregation build above
                                                     // the 'flatMap' emits each of these aggregation list as a single item

                     .map { it.collect {  it instanceof Collection ? it.sort() : it }   }

   merge(aggregation)
}