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%)

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0.0

/demux/cli/indexreport.py

import click
import logging

from pathlib import Path

from demux.constants import REFERENCE_REPORT_HEADER, REPORT_TABLES_INDEX
from demux.utils.indexreport import IndexReport


LOG = logging.getLogger(__name__)


@click.group()
def indexreport():
    """Index report commands"""


@indexreport.command()
@click.option(
    "--cluster-counts",
    type=int,
    default=1000000,
    help=(
        f"Cluster count cut-off, any samples (besides indexcheck ones) with lower cluster counts are"
        f" included in the summary"
    ),
)
@click.option(
    "--dry-run", help="Dry of the function, will not write any report", is_flag=True
)
@click.option(
    "--index-report-path",
    type=str,
    required=True,
    help="Path to bcl2fastq indexcheck report (laneBarcode.html)",
)
@click.option(
    "--out-dir",
    type=str,
    required=True,
    help="Path of outdirectory for summary report",
)
@click.option(
    "--run-parameters-path",
    type=str,
    required=True,
    help="Path to RunParameters.xml file for the flowcell",
)
def summary(
    cluster_counts: int,
    dry_run: bool,
    index_report_path: str,
    out_dir: str,
    run_parameters_path: str,
):
    """Create a summary of the indexcheck report, extracting information on samples with low number of clusters
    and the topmost common unknown indexes"""
    index_report = IndexReport(
        cluster_counts=cluster_counts,
        index_report_path=Path(index_report_path),
        out_dir=Path(out_dir),
        report_tables_index=REPORT_TABLES_INDEX,
        run_parameters_path=Path(run_parameters_path),
    )
    LOG.info(f"Creating summary of laneBarcode.html for FC: {index_report.flowcell_id}")
    index_report.validate(reference_report_header=REFERENCE_REPORT_HEADER)
    if not dry_run:
        index_report.write_summary(report_tables_index=REPORT_TABLES_INDEX)
    else:
        LOG.info("This is a dry-run, will not write a summary report")

1	import click	×
2	import logging	×
3
4	from pathlib import Path	×
5
6	from demux.constants import REFERENCE_REPORT_HEADER, REPORT_TABLES_INDEX	×
7	from demux.utils.indexreport import IndexReport	×
8
9
10	LOG = logging.getLogger(__name__)	×
11
12
13	@click.group()	×
14	def indexreport():
15	"""Index report commands"""
16
17
18	@indexreport.command()	×
19	@click.option(	×
20	"--cluster-counts",
21	type=int,
22	default=1000000,
23	help=(
24	f"Cluster count cut-off, any samples (besides indexcheck ones) with lower cluster counts are"
25	f" included in the summary"
26	),
27	)
28	@click.option(	×
29	"--dry-run", help="Dry of the function, will not write any report", is_flag=True
30	)
31	@click.option(	×
32	"--index-report-path",
33	type=str,
34	required=True,
35	help="Path to bcl2fastq indexcheck report (laneBarcode.html)",
36	)
37	@click.option(	×
38	"--out-dir",
39	type=str,
40	required=True,
41	help="Path of outdirectory for summary report",
42	)
43	@click.option(	×
44	"--run-parameters-path",
45	type=str,
46	required=True,
47	help="Path to RunParameters.xml file for the flowcell",
48	)
49	def summary(	×
50	cluster_counts: int,
51	dry_run: bool,
52	index_report_path: str,
53	out_dir: str,
54	run_parameters_path: str,
55	):
56	"""Create a summary of the indexcheck report, extracting information on samples with low number of clusters
57	and the topmost common unknown indexes"""
58	index_report = IndexReport(	×
59	cluster_counts=cluster_counts,
60	index_report_path=Path(index_report_path),
61	out_dir=Path(out_dir),
62	report_tables_index=REPORT_TABLES_INDEX,
63	run_parameters_path=Path(run_parameters_path),
64	)
65	LOG.info(f"Creating summary of laneBarcode.html for FC: {index_report.flowcell_id}")	×
66	index_report.validate(reference_report_header=REFERENCE_REPORT_HEADER)	×
67	if not dry_run:	×
68	index_report.write_summary(report_tables_index=REPORT_TABLES_INDEX)	×
69	else:
70	LOG.info("This is a dry-run, will not write a summary report")	×

Clinical-Genomics / demultiplexing / 4627485829

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