from enum import Enum
from typing import Optional
from flytekit.core.launch_plan import reference_launch_plan
from ..types.directory import LatchDir
from ..types.file import LatchFile
[docs]class BaseQualityEncoding(Enum):
phred33 = "--phred33"
phred64 = "--phred64"
[docs]class AdapterSequence(Enum):
auto = "auto"
illumina = "--illumina"
stranded_illumina = "--stranded_illumina"
nextera = "--nextera"
small_rna = "--small_rna"
@reference_launch_plan(
project="1656",
domain="development",
name="wf.__init__.trim_galore",
version="0.0.12-bcecec",
)
def trim_galore(
input_forward: LatchFile,
input_reverse: LatchFile,
base_out: Optional[str],
output_directory: Optional[LatchDir],
fastqc_args: Optional[str],
adapter: Optional[str],
adapter2: Optional[str],
consider_already_trimmed: Optional[int],
max_length: Optional[int],
max_n: Optional[float],
clip_R1: Optional[int],
clip_R2: Optional[int],
three_prime_clip_R1: Optional[int],
three_prime_clip_R2: Optional[int],
hardtrim5: Optional[int],
hardtrim3: Optional[int],
quality: int = 20,
base_quality_encoding: BaseQualityEncoding = BaseQualityEncoding.phred33,
fastqc: bool = True,
adapter_sequence: AdapterSequence = AdapterSequence.auto,
stringency: int = 1,
error_rate: float = 0.01,
gzip_output_files: bool = False,
length: int = 20,
trim_n: bool = False,
report_file: bool = True,
polyA: bool = False,
implicon: bool = False,
retain_unpaired: bool = True,
length_1: int = 35,
length_2: int = 35,
) -> LatchDir: ...