10157044146

Committed 30 Jul 2024 06:07AM UTC coverage: 84.32%. First build

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github

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Commit Message

Merge 7f53bce07 into 36c50aa67

Run Details

10 of 47 new or added lines in 3 files covered. (21.28%)

21113 of 25039 relevant lines covered (84.32%)

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0.0

/cg/cli/post_process/post_process.py

1	"""CLI commands to post-process a sequencing run."""
2
NEW 3	import logging	×
4
NEW 5	import click	×
6
NEW 7	from cg.cli.post_process.utils import get_post_processing_service_from_run_name	×
NEW 8	from cg.cli.utils import CLICK_CONTEXT_SETTINGS	×
NEW 9	from cg.models.cg_config import CGConfig	×
NEW 10	from cg.services.post_processing.abstract_classes import PostProcessingService	×
11
NEW 12	LOG = logging.getLogger(__name__)	×
13
14
NEW 15	@click.group(name="post-process", context_settings=CLICK_CONTEXT_SETTINGS)	×
NEW 16	def post_process_group():	×
17	"""Finish up after demultiplexing."""
18
19
NEW 20	@post_process_group.command(name="run")	×
NEW 21	@click.argument("run-name")	×
NEW 22	@click.pass_obj	×
NEW 23	def post_process_sequencing_run(context: CGConfig, run_name: str):	×
24	"""Command to post-process a sequencing run from any device.
25
26	run-name is the full name of the sequencing unit of run. For example:
27	PacBio: 'r84202_20240522_133539/1_A01'
28	"""
NEW 29	post_processing_service: PostProcessingService = get_post_processing_service_from_run_name(	×
30	context=context, run_name=run_name
31	)
NEW 32	post_processing_service.post_process(	×
33	run_name=run_name, sequencing_dir=context.run_instruments.pacbio.data_dir
34	)