KeyError while preparing assembly SampleSheet

[dfornika]

We've run into an error:

Traceback (most recent call last):
  File "auto-cpo/bin/auto-cpo", line 33, in <module>
    sys.exit(load_entry_point('auto-cpo', 'console_scripts', 'auto-cpo')())
  File "auto-cpo/auto_cpo/__main__.py", line 62, in main
    core.analyze_run(config, run, "short")
  File "auto-cpo/auto_cpo/core.py", line 327, in analyze_run
    writer.writerow(library_fastq_paths[library_id])
KeyError: '<SAMPLE_ID>'

The context is:

auto-cpo/auto_cpo/core.py

Lines 318 to 327 in ee7ba4e

	library_fastq_paths = get_library_fastq_paths(run['analysis_parameters']['fastq_input'])
	assembly_samplesheet_path = os.path.join(samplesheets_dir, analysis_run_id + '_routine-assembly_samplesheet.csv')
	with open(assembly_samplesheet_path, 'w') as f:
	output_fieldnames = ['ID', 'R1', 'R2']
	writer = csv.DictWriter(f, fieldnames=output_fieldnames, dialect='unix', quoting=csv.QUOTE_MINIMAL)
	writer.writeheader()
	for library_id, library_qc in total_bases_by_library.items():
	pass_fail = library_qc['total_bases_input_pass_fail']
	if pass_fail == "PASS" or pass_fail == "WARN":
	writer.writerow(library_fastq_paths[library_id])

This function also relevant:

auto-cpo/auto_cpo/core.py

Lines 118 to 143 in ee7ba4e

	def get_library_fastq_paths(fastq_input_dir: str):
	"""
	Get the paths to all of the fastq files in a directory.
	param: fastq_input_dir: Path to a directory containing fastq files.
	type: fastq_input_dir: str
	return: Paths to R1 and R2 fastq files, indexed by library ID. Keys of the dict are library IDs, values are dicts with keys: ['ID', 'R1', 'R2'].
	rtype: dict[str, dict[str, str]]
	"""
	fastq_paths_by_library_id = {}
	for fastq_file in glob.glob(os.path.join(fastq_input_dir, '*.f*q.gz')):
	fastq_file_basename = os.path.basename(fastq_file)
	fastq_file_abspath = os.path.abspath(fastq_file)
	fastq_file_basename_parts = fastq_file_basename.split('_')
	library_id = fastq_file_basename_parts[0]
	if library_id not in fastq_paths_by_library_id:
	fastq_paths_by_library_id[library_id] = {
	'ID': library_id,
	'R1': None,
	'R2': None,
	}
	if '_R1' in fastq_file_basename:
	fastq_paths_by_library_id[library_id]['R1'] = fastq_file_abspath
	elif '_R2' in fastq_file_basename:
	fastq_paths_by_library_id[library_id]['R2'] = fastq_file_abspath
	return fastq_paths_by_library_id