text: #!/usr/bin/env python
  
  # TODO nf-core: Update the script to check the samplesheet
  # This script is based on the example at: https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
  
  import os
  import sys
  import errno
  import argparse
  
  
  def parse_args(args=None):
      Description = "Reformat nf-core/mlst samplesheet file and check its contents."
      Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
  
      parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
      parser.add_argument("FILE_IN", help="Input samplesheet file.")
      parser.add_argument("FILE_OUT", help="Output file.")
      return parser.parse_args(args)
  
  
  def make_dir(path):
      if len(path) > 0:
          try:
              os.makedirs(path)
          except OSError as exception:
              if exception.errno != errno.EEXIST:
                  raise exception
  
  
  def print_error(error, context="Line", context_str=""):
      error_str = "ERROR: Please check samplesheet -> {}".format(error)
      if context != "" and context_str != "":
          error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format(
              error, context.strip(), context_str.strip()
          )
      print(error_str)
      sys.exit(1)
  
  
  # TODO nf-core: Update the check_samplesheet function
  def check_samplesheet(file_in, file_out):
      """
      This function checks that the samplesheet follows the following structure:
  
      sample,fastq_1,fastq_2
      SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz
      SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz
      SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,
  
      For an example see:
      https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
      """
  
      sample_mapping_dict = {}
      with open(file_in, "r") as fin:
  
          ## Check header
          MIN_COLS = 2
          # TODO nf-core: Update the column names for the input samplesheet
          HEADER = ["sample", "fastq_1", "fastq_2"]
          header = [x.strip('"') for x in fin.readline().strip().split(",")]
          if header[: len(HEADER)] != HEADER:
              print("ERROR: Please check samplesheet header -> {} != {}".format(",".join(header), ",".join(HEADER)))
              sys.exit(1)
  
          ## Check sample entries
          for line in fin:
              lspl = [x.strip().strip('"') for x in line.strip().split(",")]
  
              # Check valid number of columns per row
              if len(lspl) < len(HEADER):
                  print_error(
                      "Invalid number of columns (minimum = {})!".format(len(HEADER)),
                      "Line",
                      line,
                  )
              num_cols = len([x for x in lspl if x])
              if num_cols < MIN_COLS:
                  print_error(
                      "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
                      "Line",
                      line,
                  )
  
              ## Check sample name entries
              sample, fastq_1, fastq_2 = lspl[: len(HEADER)]
              sample = sample.replace(" ", "_")
              if not sample:
                  print_error("Sample entry has not been specified!", "Line", line)
  
              ## Check FastQ file extension
              for fastq in [fastq_1, fastq_2]:
                  if fastq:
                      if fastq.find(" ") != -1:
                          print_error("FastQ file contains spaces!", "Line", line)
                      if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
                          print_error(
                              "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
                              "Line",
                              line,
                          )
  
              ## Auto-detect paired-end/single-end
              sample_info = []  ## [single_end, fastq_1, fastq_2]
              if sample and fastq_1 and fastq_2:  ## Paired-end short reads
                  sample_info = ["0", fastq_1, fastq_2]
              elif sample and fastq_1 and not fastq_2:  ## Single-end short reads
                  sample_info = ["1", fastq_1, fastq_2]
              else:
                  print_error("Invalid combination of columns provided!", "Line", line)
  
              ## Create sample mapping dictionary = { sample: [ single_end, fastq_1, fastq_2 ] }
              if sample not in sample_mapping_dict:
                  sample_mapping_dict[sample] = [sample_info]
              else:
                  if sample_info in sample_mapping_dict[sample]:
                      print_error("Samplesheet contains duplicate rows!", "Line", line)
                  else:
                      sample_mapping_dict[sample].append(sample_info)
  
      ## Write validated samplesheet with appropriate columns
      if len(sample_mapping_dict) > 0:
          out_dir = os.path.dirname(file_out)
          make_dir(out_dir)
          with open(file_out, "w") as fout:
              fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n")
              for sample in sorted(sample_mapping_dict.keys()):
  
                  ## Check that multiple runs of the same sample are of the same datatype
                  if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]):
                      print_error("Multiple runs of a sample must be of the same datatype!", "Sample: {}".format(sample))
  
                  for idx, val in enumerate(sample_mapping_dict[sample]):
                      fout.write(",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n")
      else:
          print_error("No entries to process!", "Samplesheet: {}".format(file_in))
  
  
  def main(args=None):
      args = parse_args(args)
      check_samplesheet(args.FILE_IN, args.FILE_OUT)
  
  
  if __name__ == "__main__":
      sys.exit(main())
  