10403793760

Committed 15 Aug 2024 12:30PM UTC coverage: 84.729%. First build

Build # 10403793760

Build Type

Pull #3453

github

Committed by

web-flow

Commit Message

Merge 063bd25cf into bcd8941ea

Pull Request Pull Request #3453: feature(dev-branch-pacbio)

Run Details

532 of 581 new or added lines in 34 files covered. (91.57%)

21683 of 25591 relevant lines covered (84.73%)

0.85 hits per line

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85.0

/cg/cli/post_process/post_process.py

"""CLI commands to post-process a sequencing run."""

import logging

import click

from cg.cli.post_process.utils import get_post_processing_service_from_run_name
from cg.cli.utils import CLICK_CONTEXT_SETTINGS
from cg.constants.cli_options import DRY_RUN
from cg.models.cg_config import CGConfig
from cg.services.run_devices.abstract_classes import PostProcessingService

LOG = logging.getLogger(__name__)


@click.group(name="post-process", context_settings=CLICK_CONTEXT_SETTINGS)
def post_process_group():
    """Post-process sequencing runs from the sequencing instruments."""
    LOG.info("Running cg post-processing.")


@post_process_group.command(name="run")
@DRY_RUN
@click.argument("run-name")
@click.pass_obj
def post_process_sequencing_run(context: CGConfig, run_name: str, dry_run: bool):
    """Post-process a sequencing run from the PacBio instrument.

    run-name is the full name of the sequencing unit of run. For example:
        PacBio: 'r84202_20240522_133539/1_A01'
    """
    post_processing_service: PostProcessingService = get_post_processing_service_from_run_name(
        context=context, run_name=run_name
    )
    post_processing_service.post_process(run_name=run_name, dry_run=dry_run)


post_process_group: click.Group
post_process_group.add_command(post_process_sequencing_run)

1	"""CLI commands to post-process a sequencing run."""
2
3	import logging	1✔
4
5	import click	1✔
6
7	from cg.cli.post_process.utils import get_post_processing_service_from_run_name	1✔
8	from cg.cli.utils import CLICK_CONTEXT_SETTINGS	1✔
9	from cg.constants.cli_options import DRY_RUN	1✔
10	from cg.models.cg_config import CGConfig	1✔
11	from cg.services.run_devices.abstract_classes import PostProcessingService	1✔
12
13	LOG = logging.getLogger(__name__)	1✔
14
15
16	@click.group(name="post-process", context_settings=CLICK_CONTEXT_SETTINGS)	1✔
17	def post_process_group():	1✔
18	"""Post-process sequencing runs from the sequencing instruments."""
NEW 19	LOG.info("Running cg post-processing.")	×
20
21
22	@post_process_group.command(name="run")	1✔
23	@DRY_RUN	1✔
24	@click.argument("run-name")	1✔
25	@click.pass_obj	1✔
26	def post_process_sequencing_run(context: CGConfig, run_name: str, dry_run: bool):	1✔
27	"""Post-process a sequencing run from the PacBio instrument.
28
29	run-name is the full name of the sequencing unit of run. For example:
30	PacBio: 'r84202_20240522_133539/1_A01'
31	"""
NEW 32	post_processing_service: PostProcessingService = get_post_processing_service_from_run_name(	×
33	context=context, run_name=run_name
34	)
NEW 35	post_processing_service.post_process(run_name=run_name, dry_run=dry_run)	×
36
37
38	post_process_group: click.Group	1✔
39	post_process_group.add_command(post_process_sequencing_run)	1✔

Clinical-Genomics / cg / 10403793760

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