cg 82.0.6__tar.gz → 83.13.0__tar.gz

{cg-82.0.6 → cg-83.13.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 82.0.6
+Version: 83.13.0
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

cg-83.13.0/cg/__init__.py

@@ -0,0 +1,2 @@
+__title__ = "cg"
+__version__ = "83.13.0"

{cg-82.0.6 → cg-83.13.0}/cg/apps/housekeeper/hk.py

@@ -120,7 +120,7 @@ class HousekeeperAPI:
         *,
         bundle: str = None,
         tags: set[str] = None,
-        version: int = None,
+        version: int | None = None,
         path: str = None,
     ) -> Query:
         """Fetch files."""

{cg-82.0.6 → cg-83.13.0}/cg/apps/tb/api.py

@@ -134,7 +134,7 @@ class TrailblazerAPI:
         self,
         case_id: str,
         analysis_type: str,
-        config_path: str,
+        config_path: str | None,
         out_dir: str,
         priority: TrailblazerPriority,
         workflow: Workflow,

{cg-82.0.6 → cg-83.13.0}/cg/cli/upload/mutacc.py

@@ -7,7 +7,7 @@ import rich_click as click
 from cg.apps.mutacc_auto import MutaccAutoAPI
 from cg.apps.scout.scout_export import ScoutExportCase
 from cg.apps.scout.scoutapi import ScoutAPI
-from cg.cli.upload.utils import get_scout_api
+from cg.cli.upload.utils import get_scout_api_by_genome_build
 from cg.constants.cli_options import DRY_RUN
 from cg.meta.upload.mutacc import UploadToMutaccAPI
 from cg.models.cg_config import CGConfig
@@ -19,17 +19,30 @@ LOG = logging.getLogger(__name__)
 @click.option("-c", "--case-id", help="internal case id, leave empty to process all")
 @click.option("-d", "--days-ago", type=int, default=1, help="days since solved")
 @click.option("-C", "--customers", type=str, multiple=True, help="Filter on customers")
+@click.option(
+    "--scout-instance",
+    type=click.Choice(["hg19", "hg38"]),
+    help="Which scout instance to fetch cases from",
+    required=True,
+)
 @DRY_RUN
 @click.pass_obj
 def process_solved(
-    context: CGConfig, case_id: str | None, days_ago: int, customers: tuple[str], dry_run: bool
+    context: CGConfig,
+    scout_instance: str,
+    case_id: str | None,
+    days_ago: int,
+    customers: tuple[str],
+    dry_run: bool,
 ):
     """Process cases with mutacc that has been marked as solved in scout.
     This prepares them to be uploaded to the mutacc database"""
 
     LOG.info("----------------- PROCESS-SOLVED ----------------")
 
-    scout_api: ScoutAPI = get_scout_api(cg_config=context, case_id=case_id)
+    scout_api: ScoutAPI = get_scout_api_by_genome_build(
+        cg_config=context, genome_build=scout_instance
+    )
     mutacc_auto_api: MutaccAutoAPI = context.mutacc_auto_api
     mutacc_upload_api = UploadToMutaccAPI(scout_api=scout_api, mutacc_auto_api=mutacc_auto_api)
 

{cg-82.0.6 → cg-83.13.0}/cg/cli/upload/scout.py

@@ -8,7 +8,7 @@ from housekeeper.store.models import File, Version
 
 from cg.apps.housekeeper.hk import HousekeeperAPI
 from cg.apps.scout.scoutapi import ScoutAPI
-from cg.cli.upload.utils import get_scout_api, suggest_cases_to_upload
+from cg.cli.upload.utils import get_scout_api_by_case, suggest_cases_to_upload
 from cg.constants import Workflow
 from cg.constants.cli_options import DRY_RUN
 from cg.constants.constants import FileFormat
@@ -145,7 +145,7 @@ def upload_case_to_scout(context: CGConfig, re_upload: bool, dry_run: bool, case
     LOG.info("----------------- UPLOAD -----------------------")
 
     housekeeper_api: HousekeeperAPI = context.housekeeper_api
-    scout_api: ScoutAPI = get_scout_api(cg_config=context, case_id=case_id)
+    scout_api: ScoutAPI = get_scout_api_by_case(cg_config=context, case_id=case_id)
 
     tag_name: str = UploadScoutAPI.get_load_config_tag()
     version: Version = housekeeper_api.last_version(bundle=case_id)

{cg-82.0.6 → cg-83.13.0}/cg/cli/upload/utils.py

@@ -24,6 +24,15 @@ def suggest_cases_to_upload(status_db: Store, workflow: Workflow | None = None)
         click.echo(case_obj)
 
 
-def get_scout_api(cg_config: CGConfig, case_id: str) -> ScoutAPI:
+def get_scout_api_by_case(cg_config: CGConfig, case_id: str) -> ScoutAPI:
     workflow = cg_config.status_db.get_case_by_internal_id(case_id).data_analysis
     return cg_config.scout_api_38 if workflow == Workflow.NALLO else cg_config.scout_api_37
+
+
+def get_scout_api_by_genome_build(cg_config: CGConfig, genome_build: str) -> ScoutAPI:
+    """Return the appropriate ScoutAPI based on the genome build."""
+    if genome_build == "hg38":
+        return cg_config.scout_api_38
+    if genome_build == "hg19":
+        return cg_config.scout_api_37
+    raise ValueError(f"Unsupported genome build: {genome_build}")

{cg-82.0.6 → cg-83.13.0}/cg/cli/workflow/balsamic/base.py

@@ -140,7 +140,12 @@ def store_available(context: click.Context, dry_run: bool) -> None:
 @ARGUMENT_CASE_ID
 @click.pass_obj
 def config_case(cg_config: CGConfig, case_id: str, panel_bed: str | None):
-    """Configure a Balsamic case so that it is ready to be run."""
+    """Configure a Balsamic case so that it is ready to be run.
+
+    \b
+    Creates the case config file:
+        - CASE_ID.json
+    """
     factory = ConfiguratorFactory(cg_config)
     configurator = cast(BalsamicConfigurator, factory.get_configurator(Workflow.BALSAMIC))
     configurator.configure(case_id=case_id, panel_bed=panel_bed)
@@ -151,7 +156,13 @@ def config_case(cg_config: CGConfig, case_id: str, panel_bed: str | None):
 @ARGUMENT_CASE_ID
 @click.pass_obj
 def run(cg_config: CGConfig, case_id: str, workflow_profile: click.Path | None):
-    """Run a preconfigured Balsamic case."""
+    """
+    Run a preconfigured Balsamic case.
+
+    \b
+    Assumes that case config file exist in the case run directory:
+        - CASE_ID.json
+    """
     factory = AnalysisStarterFactory(cg_config)
     analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(Workflow.BALSAMIC)
     analysis_starter.run(case_id=case_id, workflow_profile=workflow_profile)
@@ -168,7 +179,14 @@ def start(
     panel_bed: str | None,
     workflow_profile: click.Path | None,
 ):
-    """Start a Balsamic case. Configures the case if needed."""
+    """
+    Starts a Balsamic cases.
+
+    \b
+    Configures the case and creates the case config file:
+        - CASE_ID.json
+    and submits the job to slurm.
+    """
     factory = AnalysisStarterFactory(cg_config)
     analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(Workflow.BALSAMIC)
     analysis_starter.start(case_id=case_id, workflow_profile=workflow_profile, panel_bed=panel_bed)
@@ -177,7 +195,14 @@ def start(
 @balsamic.command("start-available")
 @click.pass_obj
 def start_available(cg_config: CGConfig):
-    """Starts all available raredisease cases."""
+    """
+    Starts all available Balsamic cases.
+
+    \b
+    Configures the individual case and creates its case config file:
+        - CASE_ID.json
+    and submits the job to slurm.
+    """
     LOG.info("Starting Balsamic workflow for all available cases.")
     factory = AnalysisStarterFactory(cg_config)
     analysis_starter = factory.get_analysis_starter_for_workflow(Workflow.BALSAMIC)

{cg-82.0.6 → cg-83.13.0}/cg/cli/workflow/microsalt/base.py

@@ -41,7 +41,9 @@ microsalt.add_command(resolve_compression)
 @ARGUMENT_CASE_ID
 @click.pass_obj
 def config_case(cg_config: CGConfig, case_id: str) -> None:
-    """Create a config file for a microSALT case."""
+    """
+    Configure a microSALT case so that it is ready to be run.
+    """
     factory = ConfiguratorFactory(cg_config)
     configurator = cast(MicrosaltConfigurator, factory.get_configurator(Workflow.MICROSALT))
     configurator.configure(case_id=case_id)

{cg-82.0.6 → cg-83.13.0}/cg/cli/workflow/nallo/base.py

@@ -5,7 +5,7 @@ from typing import cast
 
 import rich_click as click
 
-from cg.cli.utils import CLICK_CONTEXT_SETTINGS, echo_lines
+from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 from cg.cli.workflow.commands import ARGUMENT_CASE_ID
 from cg.cli.workflow.nf_analysis import (
     OPTION_RESUME,
@@ -16,7 +16,6 @@ from cg.cli.workflow.nf_analysis import (
     store_available,
     store_housekeeper,
 )
-from cg.constants.cli_options import DRY_RUN
 from cg.constants.constants import MetaApis, Workflow
 from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.nallo import NalloAnalysisAPI
@@ -44,29 +43,14 @@ nallo.add_command(store_housekeeper)
 nallo.add_command(metrics_deliver)
 
 
-@nallo.command("panel")
-@DRY_RUN
-@ARGUMENT_CASE_ID
-@click.pass_obj
-def panel(context: CGConfig, case_id: str, dry_run: bool) -> None:
-    """Write aggregated gene panel file exported from Scout."""
-
-    analysis_api: NalloAnalysisAPI = context.meta_apis["analysis_api"]
-    analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
-
-    bed_lines: list[str] = analysis_api.get_gene_panel(case_id=case_id)
-    if dry_run:
-        echo_lines(lines=bed_lines)
-        return
-    analysis_api.write_panel_as_tsv(case_id=case_id, content=bed_lines)
-
-
 @nallo.command("config-case")
 @ARGUMENT_CASE_ID
 @click.pass_obj
 def config_case(cg_config: CGConfig, case_id: str):
     """
-    Configure a Nallo case so that it is ready to be run. \b
+    Configure a Nallo case so that it is ready to be run.
+
+    \b
     Creates the following files in the case run directory:
         - CASE_ID_params_file.yaml
         - CASE_ID_nextflow_config.json
@@ -84,7 +68,9 @@ def config_case(cg_config: CGConfig, case_id: str):
 @click.pass_obj
 def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None) -> None:
     """
-    Run a preconfigured Nallo case. \b
+    Run a preconfigured Nallo case.
+
+    \b
     Assumes that the following files exist in the case run directory:
         - CASE_ID_params_file.yaml
         - CASE_ID_nextflow_config.json
@@ -101,7 +87,9 @@ def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None) -
 @click.pass_obj
 def start(cg_config: CGConfig, case_id: str, revision: str | None):
     """
-    Start a Nallo case. \b
+    Start a Nallo case.
+
+    \b
     Configures the case and writes the following files:
         - CASE_ID_params_file.yaml
         - CASE_ID_nextflow_config.json

cg-83.13.0/cg/cli/workflow/nf_analysis.py

@@ -0,0 +1,135 @@
+"""CLI options for Nextflow and NF-Tower."""
+
+import logging
+
+import rich_click as click
+
+from cg.cli.workflow.commands import ARGUMENT_CASE_ID
+from cg.cli.workflow.utils import validate_force_store_option
+from cg.constants.cli_options import COMMENT, DRY_RUN, FORCE
+from cg.constants.constants import MetaApis
+from cg.exc import CgError, HousekeeperStoreError
+from cg.meta.workflow.nf_analysis import NfAnalysisAPI
+from cg.models.cg_config import CGConfig
+
+LOG = logging.getLogger(__name__)
+
+
+OPTION_RESUME = click.option(
+    "--resume",
+    default=True,
+    show_default=True,
+    help="Execute the script using the cached results, useful to continue "
+    "executions that were stopped by an error",
+)
+OPTION_REVISION = click.option(
+    "--revision",
+    type=str,
+    help="Revision of workflow to run (either a git branch, tag or commit SHA number)",
+)
+
+
+@click.command("metrics-deliver")
+@ARGUMENT_CASE_ID
+@DRY_RUN
+@click.pass_obj
+def metrics_deliver(context: CGConfig, case_id: str, dry_run: bool) -> None:
+    """
+    Create and validate a metrics deliverables file for given case id.
+    If QC metrics are met it sets the status in Trailblazer to complete.
+    If failed, it sets it as failed and adds a comment with information of the failed metrics.
+    """
+    analysis_api: NfAnalysisAPI = context.meta_apis[MetaApis.ANALYSIS_API]
+    try:
+        analysis_api.metrics_deliver(case_id=case_id, dry_run=dry_run)
+    except CgError as error:
+        raise click.Abort() from error
+
+
+@click.command("report-deliver")
+@ARGUMENT_CASE_ID
+@DRY_RUN
+@FORCE
+@click.pass_obj
+def report_deliver(context: CGConfig, case_id: str, dry_run: bool, force: bool) -> None:
+    """
+    Create a Housekeeper deliverables file for a given case ID.
+
+    Raises:
+        click.Abort: If an error occurs during the deliverables report generation or validation.
+    """
+    analysis_api: NfAnalysisAPI = context.meta_apis[MetaApis.ANALYSIS_API]
+    try:
+        analysis_api.report_deliver(case_id=case_id, dry_run=dry_run, force=force)
+    except CgError as error:
+        LOG.error(f"Could not create report file: {error}")
+        raise click.Abort()
+
+
+@click.command("store-housekeeper")
+@ARGUMENT_CASE_ID
+@DRY_RUN
+@FORCE
+@click.pass_obj
+def store_housekeeper(context: CGConfig, case_id: str, dry_run: bool, force: bool) -> None:
+    """
+    Store a finished NF-analysis in Housekeeper.
+
+    Raises:
+        click.Abort: If an error occurs while storing a case bundle in Housekeeper.
+    """
+    analysis_api: NfAnalysisAPI = context.meta_apis[MetaApis.ANALYSIS_API]
+    try:
+        analysis_api.store_analysis_housekeeper(case_id=case_id, dry_run=dry_run, force=force)
+    except HousekeeperStoreError as error:
+        LOG.error(f"Could not store bundle in Housekeeper and StatusDB: {error}!")
+        raise click.Abort()
+
+
+@click.command("store")
+@ARGUMENT_CASE_ID
+@COMMENT
+@DRY_RUN
+@FORCE
+@click.pass_context
+def store(
+    context: click.Context, case_id: str, comment: str | None, dry_run: bool, force: bool
+) -> None:
+    """
+    Store deliverable files in Housekeeper after meeting QC metrics criteria.
+
+    Raises:
+        click.Abort: If an error occurs during the deliverables file generation, metrics
+        validation, or storage processes.
+    """
+    validate_force_store_option(force=force, comment=comment)
+    analysis_api: NfAnalysisAPI = context.obj.meta_apis[MetaApis.ANALYSIS_API]
+    try:
+        analysis_api.store(case_id=case_id, comment=comment, dry_run=dry_run, force=force)
+    except Exception as error:
+        LOG.error(repr(error))
+        raise click.Abort()
+
+
+@click.command("store-available")
+@DRY_RUN
+@click.pass_context
+def store_available(context: click.Context, dry_run: bool) -> None:
+    """
+    Store finished analyses for cases marked as running in StatusDB and completed or QC in Trailblazer.
+
+    Raises:
+        click.Abort: If any error occurs during the storage process.
+    """
+
+    analysis_api: NfAnalysisAPI = context.obj.meta_apis[MetaApis.ANALYSIS_API]
+    was_successful: bool = True
+    for case in analysis_api.get_cases_to_store():
+        LOG.info(f"Storing deliverables for {case.internal_id}")
+        try:
+            analysis_api.store(case_id=case.internal_id, dry_run=dry_run)
+        except Exception as error:
+            LOG.error(f"Error storing {case.internal_id}: {repr(error)}")
+            was_successful = False
+    if not was_successful:
+        raise click.Abort()

{cg-82.0.6 → cg-83.13.0}/cg/cli/workflow/raredisease/base.py

@@ -49,7 +49,9 @@ raredisease.add_command(store_housekeeper)
 @click.pass_obj
 def config_case(cg_config: CGConfig, case_id: str):
     """
-    Configure a raredisease case so that it is ready to be run. \b
+    Configure a raredisease case so that it is ready to be run.
+
+    \b
     Creates the following files in the case run directory:
         - CASE_ID_params_file.yaml
         - CASE_ID_nextflow_config.json
@@ -67,7 +69,9 @@ def config_case(cg_config: CGConfig, case_id: str):
 @click.pass_obj
 def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None):
     """
-    Run a preconfigured raredisease case. \b
+    Run a preconfigured raredisease case.
+
+    \b
     Assumes that the following files exist in the case run directory:
         - CASE_ID_params_file.yaml
         - CASE_ID_nextflow_config.json
@@ -86,7 +90,9 @@ def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None):
 @click.pass_obj
 def start(cg_config: CGConfig, case_id: str, revision: str | None):
     """
-    Start a raredisease case. \b
+    Start a raredisease case.
+
+    \b
     Configures the case and writes the following files:
         - CASE_ID_params_file.yaml
         - CASE_ID_nextflow_config.json

{cg-82.0.6 → cg-83.13.0}/cg/cli/workflow/rnafusion/base.py

@@ -48,7 +48,15 @@ rnafusion.add_command(store_available)
 @ARGUMENT_CASE_ID
 @click.pass_obj
 def config_case(cg_config: CGConfig, case_id: str):
-    """Configure an RNAFUSION case so that it is ready to be run."""
+    """
+    Configure an RNAFUSION case so that it is ready to be run.
+
+    \b
+    Creates the following files in the case run directory:
+        - CASE_ID_params_file.yaml
+        - CASE_ID_nextflow_config.json
+        - CASE_ID_samplesheet.csv
+    """
     factory = ConfiguratorFactory(cg_config)
     configurator = cast(NextflowConfigurator, factory.get_configurator(Workflow.RNAFUSION))
     configurator.configure(case_id=case_id)
@@ -60,7 +68,15 @@ def config_case(cg_config: CGConfig, case_id: str):
 @ARGUMENT_CASE_ID
 @click.pass_obj
 def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None):
-    """Run a preconfigured RNAFUSION case."""
+    """
+    Run a preconfigured RNAFUSION case.
+
+    \b
+    Assumes that the following files exist in the case run directory:
+        - CASE_ID_params_file.yaml
+        - CASE_ID_nextflow_config.json
+        - CASE_ID_samplesheet.csv
+    """
     factory = AnalysisStarterFactory(cg_config)
     analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(
         Workflow.RNAFUSION
@@ -73,7 +89,16 @@ def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None):
 @ARGUMENT_CASE_ID
 @click.pass_obj
 def start(cg_config: CGConfig, case_id: str, revision: str | None):
-    """Start an RNAFUSION case. Configures the case if needed."""
+    """
+    Start an RNAFUSION case. Configures the case if needed.
+
+    \b
+    Configures the case and writes the following files:
+        - CASE_ID_params_file.yaml
+        - CASE_ID_nextflow_config.json
+        - CASE_ID_samplesheet.csv
+    and submits the job to the Seqera Platform.
+    """
     LOG.info(f"Starting RNAFUSION workflow for case {case_id}.")
     factory = AnalysisStarterFactory(cg_config)
     analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(

{cg-82.0.6 → cg-83.13.0}/cg/cli/workflow/taxprofiler/base.py

@@ -41,11 +41,14 @@ def taxprofiler(context: click.Context) -> None:
 @ARGUMENT_CASE_ID
 @click.pass_obj
 def start(cg_config: CGConfig, case_id: str, revision: str | None) -> None:
-    """Start a Taxprofiler case. \n
-    Configures the case and writes the following files: \n
-        - CASE_ID_params_file.yaml \n
-        - CASE_ID_nextflow_config.json \n
-        - CASE_ID_samplesheet.csv \n
+    """
+    Start a Taxprofiler case.
+
+    \b
+    Configures the case and writes the following files:
+        - CASE_ID_params_file.yaml
+        - CASE_ID_nextflow_config.json
+        - CASE_ID_samplesheet.csv
     and submits the job to the Seqera Platform.
     """
     factory = AnalysisStarterFactory(cg_config)
@@ -75,10 +78,13 @@ def start_available(cg_config: CGConfig) -> None:
 @ARGUMENT_CASE_ID
 @click.pass_obj
 def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None) -> None:
-    """Run a preconfigured Taxprofiler case. \n
-    Assumes that the following files are in the case run directory: \n
-        - CASE_ID_params_file.yaml \n
-        - CASE_ID_nextflow_config.json \n
+    """
+    Run a preconfigured Taxprofiler case.
+
+    \b
+    Assumes that the following files are in the case run directory:
+        - CASE_ID_params_file.yaml
+        - CASE_ID_nextflow_config.json
         - CASE_ID_samplesheet.csv
     """
     factory = AnalysisStarterFactory(cg_config)
@@ -92,10 +98,12 @@ def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None) -
 @ARGUMENT_CASE_ID
 @click.pass_obj
 def config_case(cg_config: CGConfig, case_id: str) -> None:
-    """Configure a Taxprofiler case so that it is ready to be run. \n
-    Creates the following files in the case run directory:\n
-        - CASE_ID_params_file.yaml \n
-        - CASE_ID_nextflow_config.json \n
+    """Configure a Taxprofiler case so that it is ready to be run.
+
+    \b
+    Creates the following files in the case run directory:
+        - CASE_ID_params_file.yaml
+        - CASE_ID_nextflow_config.json
         - CASE_ID_samplesheet.csv
     """
     factory = ConfiguratorFactory(cg_config)

{cg-82.0.6 → cg-83.13.0}/cg/cli/workflow/tomte/base.py

@@ -10,12 +10,8 @@ from cg.cli.workflow.commands import ARGUMENT_CASE_ID, resolve_compression
 from cg.cli.workflow.nf_analysis import (
     OPTION_RESUME,
     OPTION_REVISION,
-    config_case,
     metrics_deliver,
     report_deliver,
-    run,
-    start,
-    start_available,
     store,
     store_available,
     store_housekeeper,
@@ -41,10 +37,6 @@ def tomte(context: click.Context) -> None:
 
 
 tomte.add_command(resolve_compression)
-tomte.add_command(config_case)
-tomte.add_command(run)
-tomte.add_command(start)
-tomte.add_command(start_available)
 tomte.add_command(metrics_deliver)
 tomte.add_command(report_deliver)
 tomte.add_command(store_housekeeper)
@@ -52,12 +44,14 @@ tomte.add_command(store)
 tomte.add_command(store_available)
 
 
-@tomte.command("dev-config-case")
+@tomte.command("config-case")
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def dev_config_case(cg_config: CGConfig, case_id: str):
+def config_case(cg_config: CGConfig, case_id: str):
     """
-    Configure a Tomte case so that it is ready to be run. \b
+    Configure a Tomte case so that it is ready to be run.
+
+    \b
     Creates the following files in the case run directory:
         - CASE_ID_params_file.yaml
         - CASE_ID_nextflow_config.json
@@ -69,14 +63,16 @@ def dev_config_case(cg_config: CGConfig, case_id: str):
     configurator.configure(case_id=case_id)
 
 
-@tomte.command("dev-run")
+@tomte.command("run")
 @OPTION_REVISION
 @OPTION_RESUME
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def dev_run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None) -> None:
+def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None) -> None:
     """
-    Run a preconfigured Tomte case. \b
+    Run a preconfigured Tomte case.
+
+    \b
     Assumes that the following files exist in the case run directory:
         - CASE_ID_params_file.yaml
         - CASE_ID_nextflow_config.json
@@ -88,13 +84,15 @@ def dev_run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | Non
     analysis_starter.run(case_id=case_id, resume=resume, revision=revision)
 
 
-@tomte.command("dev-start")
+@tomte.command("start")
 @OPTION_REVISION
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def dev_start(cg_config: CGConfig, case_id: str, revision: str | None):
+def start(cg_config: CGConfig, case_id: str, revision: str | None):
     """
-    Start a Tomte case. \b
+    Start a Tomte case.
+
+    \b
     Configures the case and writes the following files:
         - CASE_ID_params_file.yaml
         - CASE_ID_nextflow_config.json
@@ -107,9 +105,9 @@ def dev_start(cg_config: CGConfig, case_id: str, revision: str | None):
     analysis_starter.start(case_id=case_id, revision=revision)
 
 
-@tomte.command("dev-start-available")
+@tomte.command("start-available")
 @click.pass_obj
-def dev_start_available(cg_config: CGConfig):
+def start_available(cg_config: CGConfig):
     """Starts all available Tomte cases."""
     LOG.info("Starting Tomte workflow for all available cases.")
     factory = AnalysisStarterFactory(cg_config)

{cg-82.0.6 → cg-83.13.0}/cg/constants/constants.py

@@ -100,9 +100,9 @@ class CancerAnalysisType(StrEnum):
 
 
 class SexOptions(StrEnum):
-    MALE: str = "male"
-    FEMALE: str = "female"
-    UNKNOWN: str = "unknown"
+    MALE = "male"
+    FEMALE = "female"
+    UNKNOWN = "unknown"
 
 
 SARS_COV_REGEX = "^[0-9]{2}CS[0-9]{6}$"

{cg-82.0.6 → cg-83.13.0}/cg/constants/devices.py

@@ -1,6 +1,6 @@
 """Enums for run_devices."""
 
-from enum import Enum, auto
+from enum import Enum, StrEnum, auto
 
 
 class DeviceType(Enum):
@@ -8,3 +8,8 @@ class DeviceType(Enum):
     BIONANO = auto()
     OXFORD_NANOPORE = auto()
     PACBIO = auto()
+
+
+class RevioNames(StrEnum):
+    BETTY = "Betty"
+    WILMA = "Wilma"

{cg-82.0.6 → cg-83.13.0}/cg/constants/gene_panel.py

@@ -20,6 +20,7 @@ class GenePanelMasterList(StrEnum):
     CH = "CH"
     CHILDHYPOTONIA = "CHILDHYPOTONIA"
     CTD = "CTD"
+    COMPD = "COMPD"
     DIAB = "DIAB"
     ENDO = "ENDO"
     EP = "EP"
@@ -47,7 +48,7 @@ class GenePanelMasterList(StrEnum):
     SOVM = "SOVM"
     STROKE = "STROKE"
     AID = "AID"
-    INHERITED_CANCER = "Inherited cancer"
+    IHC = "IHC"
     VEO_IBD = "VEO-IBD"
     KIDNEY = "Kidney"
     CAKUT = "CAKUT"