4627485829

Build Type

push

github-actions

Committed by karlnyr

Commit Message

remova conda stuff, expand aliases

Run Details

501 of 941 relevant lines covered (53.24%)

0.53 hits per line

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0.0

/demux/cli/base.py

"""Demultiplexing base demux command"""

import click
import coloredlogs
import logging
import yaml

from .basemask import basemask
from demux import __version__
from .indexreport import indexreport
from .samplesheet import sheet

LOG = logging.getLogger(__name__)
LEVELS = ["DEBUG", "INFO", "WARNING", "ERROR"]


@click.group()
@click.option(
    "-l",
    "--log-level",
    type=click.Choice(LEVELS),
    default="INFO",
    help="Lowest level to log at",
)
@click.option("-c", "--config", type=click.File("r"))
@click.version_option(__version__)
@click.pass_context
def demux(context, log_level, config):
    """Making demultiplexing easier!"""

    coloredlogs.install(level=log_level)
    context.obj = yaml.full_load(config) if config else {}
    context.obj["log_level"] = log_level


demux.add_command(sheet)
demux.add_command(basemask)
demux.add_command(indexreport)

1	"""Demultiplexing base demux command"""
2
3	import click	×
4	import coloredlogs	×
5	import logging	×
6	import yaml	×
7
8	from .basemask import basemask	×
9	from demux import __version__	×
10	from .indexreport import indexreport	×
11	from .samplesheet import sheet	×
12
13	LOG = logging.getLogger(__name__)	×
14	LEVELS = ["DEBUG", "INFO", "WARNING", "ERROR"]	×
15
16
17	@click.group()	×
18	@click.option(	×
19	"-l",
20	"--log-level",
21	type=click.Choice(LEVELS),
22	default="INFO",
23	help="Lowest level to log at",
24	)
25	@click.option("-c", "--config", type=click.File("r"))	×
26	@click.version_option(__version__)	×
27	@click.pass_context	×
28	def demux(context, log_level, config):
29	"""Making demultiplexing easier!"""
30
31	coloredlogs.install(level=log_level)	×
32	context.obj = yaml.full_load(config) if config else {}	×
33	context.obj["log_level"] = log_level	×
34
35
36	demux.add_command(sheet)	×
37	demux.add_command(basemask)	×
38	demux.add_command(indexreport)	×

Clinical-Genomics / demultiplexing / 4627485829

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