nextflow alignment example

gistfile1.groovy

params.path = "/path/to/data"

(reads1,reads2) = Channel.fromPath( params.path + "/**.gz").into(2)

reads1 = reads1
  .filter( ~/.+R1.+/ )
  .map { path -> ['pair_id': path.baseName[-17..-14],
  'sample_id': path.getParent().baseName,
  'read': path ] }

reads2 = reads2
  .filter( ~/.+R2.+/ )
  .map { path -> ['pair_id': path.baseName[-17..-14],
  'sample_id': path.getParent().baseName,
  'read': path ] }

read_pairs = reads1
  .phase(reads2)
  .map { pair1, pair2 -> [ pair1.pair_id, pair1.sample_id, pair1.read, pair2.read ] }
  
process alignment {
  container 'alignment'
  queue 'highmem.q'

  input:
    set pair_id, sample_id, file(read1), file(read2) from read_pairs

  output:
    set sample_id, file("alignment.bam") into alignments

  """
  align $read1 $read2 > alignment.bam
  """
}

process merge {
  container 'merge'
  queue 'all.q'
  
  input:
    set sample_id, file('alignment.bam') from alignments.groupTuple()

  output:
    set file('merged.bam') into merged

  """
  # merge all read_pair bam files into a sample bam file
  """
}