gistfile1.txt

/*
 * stitching
 */
process coordinates {

  input:
  file input_dir
  val row from ch_non_clusters.mix(ch_clusters).splitCsv(header: true, sep:'\t' )

  output:
  tuple val(cluster), base_name, coordinates_dir into ch_stitching_dataset

  shell:
  cluster = sections > 1 ? ${row.cluster} : 0
  file coordinates_dir = sections > 1 ? "${base_name}/${row.cluster}/params" : "${base_name}/params"
  '''
  some script goes here
  '''

}

process image_stitching {

  input:
  file input_dir
  tuple val(cluster), base_name, file(coordinates_dir) from ch_stitching_dataset

  output:
  file stitched_tif into ch_stitched_tif

  shell:
  tifname = sections > 1 ? "${base_name}_${row.cluster}.tif" : "${base_name}.tif"
  stitched_tif = "$base_name/$tifname"
  fovs = sections > 1 ? "--fovs \"${row.fov}\" " : ""
  '''
  !{baseDir}/bin/scripts/convert2opencv.py -i !{coordinates_dir}/FieldTables.json -o !{coordinates_dir}
  opencv-stitcher --input !{input_dir} ...
  '''

}