def run(self) -> List[str]:
delete_output_dir_if_exists(self.context.output)
# Create and save the configuration file
config = "illumiprocessor.conf"
csv = load_csv(self.context.csv_file)
config_dict = parse_illumiprocessor_config(
csv, double_index=not self.context.single_index)
dump_config_file(config, config_dict)
cmd = [
"--input",
self.context.raw_fastq,
"--output",
self.context.output,
"--cores",
str(self.context.threads),
"--config",
config,
"--log-path",
self.context.log_dir,
]
if self.context.min_len:
cmd.extend(["--min-len", str(self.context.min_len)])
if self.context.r1_pattern:
cmd.extend(["--r1-pattern", self.context.r1_pattern])
if self.context.r2_pattern:
cmd.extend(["--r2-pattern", self.context.r2_pattern])
if self.context.phred64:
cmd.extend(["--phred", "phred64"])
if self.context.single_end:
cmd.append("--se")
if self.context.no_merge:
cmd.append("--no-merge")
return self.adapters["illumiprocessor"](
cmd, capture_output=self.context.capture_output)
def config(context):
csv_file = load_csv(context["csv_file"])
config = parse_illumiprocessor_config(csv_file)
return config
def config_single_index(context):
csv_file = load_csv(context["csv_file"])
config = parse_illumiprocessor_config(csv_file, double_index=False)
return config
def test_load_csv_returns_a_list(context):
csv = load_csv(context["csv_file"])
assert isinstance(csv, list)