from collections import OrderedDict
from pathlib import Path
import yaml
import ngcloud as ng
from ngcloud.util import open, _val_bool_or_none
logger = ng._create_logger(__name__)
class Sample:
"""Sample experiment run information.
Parameters
----------
name : string
pair_end : {'R1', 'R2', False}, optional
stranded : bool, optional
Attributes
----------
name : string
Sample name. Pair-end samples should have same `name`
full_name : string
Auto-generated full sample name, containing pair-end info.
Examples
--------
If a sample is pair-end, say sample 5566 has read 1 and 2, then one should
explicitly creates two Sample instances
>>> pe = [Sample(name='5566' % pe, pair_end=pe) for pe in ['R1', 'R2']]
>>> pe
from pathlib import Path
from ngcloud import _create_logger
from ngcloud.report import Stage, Report
from ngcloud.pipe import get_shared_template_root, get_shared_static_root
from ngcloud.pipe import tuxedo
logger = _create_logger(__name__)
_here = Path(__file__).parent
class GATKBaseStage(Stage):
template_find_paths = [
_here / "report" / "templates",
get_shared_template_root(),
]
class IndexStage(GATKBaseStage):
template_entrances = 'index.html'
class QCStage(tuxedo.QCStage):
# template_find_paths = GATKBaseStage.template_find_paths
# template_find_paths.append(
# _get_builtin_template_root() / 'tuxedo'
# )
template_find_paths = (
GATKBaseStage.template_find_paths[:1] +
tuxedo.QCStage.template_find_paths
)
class AlignStage(GATKBaseStage):
template_entrances = 'align.html'
