code: def assemble_amplicon_skesa(self):
          
          with progressbar(self.metadata) as bar:
              for sample in bar:
                  # Initialise variables
                  sample[self.analysistype].skesa_outdir = os.path.join(
                      sample[self.analysistype].outputdir, self.analysistype)
                  make_path(sample[self.analysistype].skesa_outdir)
                  sample[self.analysistype].assemblyfile = os.path.join(sample[self.analysistype].skesa_outdir,
                                                                        'contigs.fasta')
                  # If there are two fastq files
                  if len(sample.general.fastqfiles) == 2:
                      # Set the reverse fastq name https://github.com/ncbi/SKESA/issues/7
                      sample[self.analysistype].spadescommand = 'skesa --fastq {fastqfiles} --cores {threads} ' \
                                                                '--use_paired_ends --vector_percent 1 ' \
                                                                '--contigs_out {contigs}'\
                          .format(fastqfiles=','.join(sample.general.fastqfiles),
                                  threads=self.cpus,
                                  contigs=sample[self.analysistype].assemblyfile)
                  # Same as above, but use single read settings for the assembler
                  else:
                      sample[self.analysistype].spadescommand = 'skesa --fastq {fastqfiles} --cores {threads} ' \
                                                                '--vector_percent 1 --contigs_out {contigs}'\
                          .format(fastqfiles=','.join(sample.general.fastqfiles),
                                  threads=self.cpus,
                                  contigs=sample[self.analysistype].assemblyfile)
                  if not os.path.isfile(sample[self.analysistype].assemblyfile):
                      # Create and run the sequence call as required
                      run_subprocess(sample[self.analysistype].spadescommand)
                      if not os.path.isfile(sample[self.analysistype].assemblyfile):
                          sample[self.analysistype].assemblyfile = 'NA'
docs: Run skesa to assemble genomes