def demultiplex_flowcell(
context: CGConfig,
dry_run: bool,
flowcell_id: str,
bcl_converter: str,
):
"""Demultiplex a flowcell on slurm using CG
flowcell-id is the flowcell run directory name, e.g. '201203_A00689_0200_AHVKJCDRXX'
"""
LOG.info("Running cg demultiplex flowcell, using %s.", bcl_converter)
flowcell_directory: Path = Path(context.demultiplex.run_dir) / flowcell_id
demultiplex_api: DemultiplexingAPI = context.demultiplex_api
demultiplex_api.set_dry_run(dry_run=dry_run)
LOG.info(f"SETTING FLOWCELL ID TO {flowcell_id}")
LOG.info(f"SETTING OUT DIR TO {demultiplex_api.out_dir}")
try:
flowcell_obj = Flowcell(flowcell_path=flowcell_directory,
bcl_converter=bcl_converter)
except FlowcellError as e:
raise click.Abort from e
delete_demux_api: DeleteDemuxAPI = DeleteDemuxAPI(
config=context,
demultiplex_base=demultiplex_api.out_dir,
dry_run=dry_run,
run_path=flowcell_directory,
)
delete_demux_api.delete_flow_cell(
cg_stats=True,
demultiplexing_dir=True,
run_dir=False,
housekeeper=True,
init_files=True,
status_db=False,
)
if not demultiplex_api.is_demultiplexing_possible(
flowcell=flowcell_obj) and not dry_run:
LOG.warning("Can not start demultiplexing!")
return
if not flowcell_obj.validate_sample_sheet():
LOG.warning(
"Malformed sample sheet. Run cg demultiplex samplesheet validate %s",
flowcell_obj.sample_sheet_path,
)
raise click.Abort
slurm_job_id: int = demultiplex_api.start_demultiplexing(
flowcell=flowcell_obj)
tb_api: TrailblazerAPI = context.trailblazer_api
demultiplex_api.add_to_trailblazer(tb_api=tb_api,
slurm_job_id=slurm_job_id,
flowcell=flowcell_obj)
def demultiplex_all(context: CGConfig, bcl_converter: str,
flowcells_directory: click.Path, dry_run: bool):
"""Demultiplex all flowcells that are ready under the flowcells_directory"""
LOG.info("Running cg demultiplex all, using %s.", bcl_converter)
if flowcells_directory:
flowcells_directory: Path = Path(str(flowcells_directory))
else:
flowcells_directory: Path = Path(context.demultiplex.run_dir)
demultiplex_api: DemultiplexingAPI = context.demultiplex_api
demultiplex_api.set_dry_run(dry_run=dry_run)
tb_api: TrailblazerAPI = context.trailblazer_api
LOG.info("Search for flowcells ready to demultiplex in %s",
flowcells_directory)
for sub_dir in flowcells_directory.iterdir():
if not sub_dir.is_dir():
continue
LOG.info("Found directory %s", sub_dir)
try:
flowcell_obj = Flowcell(flowcell_path=sub_dir,
bcl_converter=bcl_converter)
except FlowcellError:
continue
if not demultiplex_api.is_demultiplexing_possible(
flowcell=flowcell_obj) and not dry_run:
continue
if not flowcell_obj.validate_sample_sheet():
LOG.warning(
"Malformed sample sheet. Run cg demultiplex samplesheet validate %s",
flowcell_obj.sample_sheet_path,
)
continue
delete_demux_api: DeleteDemuxAPI = DeleteDemuxAPI(
config=context,
demultiplex_base=demultiplex_api.out_dir,
dry_run=dry_run,
run_path=(flowcells_directory / sub_dir),
)
delete_demux_api.delete_flow_cell(
cg_stats=False,
demultiplexing_dir=True,
run_dir=False,
housekeeper=True,
init_files=False,
status_db=False,
)
slurm_job_id: int = demultiplex_api.start_demultiplexing(
flowcell=flowcell_obj)
demultiplex_api.add_to_trailblazer(tb_api=tb_api,
slurm_job_id=slurm_job_id,
flowcell=flowcell_obj)