cg 80.1.0__py3-none-any.whl → 83.14.0__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "80.1.0"
+__version__ = "83.14.0"

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/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/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/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/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/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/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/cli/workflow/nallo/base.py

@@ -5,22 +5,17 @@ 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,
     OPTION_REVISION,
-    config_case,
     metrics_deliver,
     report_deliver,
-    run,
-    start,
-    start_available,
     store,
     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
@@ -41,40 +36,21 @@ def nallo(context: click.Context) -> None:
     context.obj.meta_apis[MetaApis.ANALYSIS_API] = NalloAnalysisAPI(config=context.obj)
 
 
-nallo.add_command(config_case)
 nallo.add_command(report_deliver)
-nallo.add_command(run)
-nallo.add_command(start)
-nallo.add_command(start_available)
 nallo.add_command(store)
 nallo.add_command(store_available)
 nallo.add_command(store_housekeeper)
 nallo.add_command(metrics_deliver)
 
 
-@nallo.command("panel")
-@DRY_RUN
+@nallo.command("config-case")
 @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("dev-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 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
@@ -85,14 +61,16 @@ def dev_config_case(cg_config: CGConfig, case_id: str):
     configurator.configure(case_id=case_id)
 
 
-@nallo.command("dev-run")
+@nallo.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 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
@@ -103,13 +81,15 @@ 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)
 
 
-@nallo.command("dev-start")
+@nallo.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 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
@@ -121,9 +101,9 @@ def dev_start(cg_config: CGConfig, case_id: str, revision: str | None):
     analysis_starter.start(case_id=case_id, revision=revision)
 
 
-@nallo.command("dev-start-available")
+@nallo.command("start-available")
 @click.pass_obj
-def dev_start_available(cg_config: CGConfig):
+def start_available(cg_config: CGConfig):
     """Starts all available Nallo cases."""
     LOG.info("Starting Nallo workflow for all available cases.")
     factory = AnalysisStarterFactory(cg_config)

cg/cli/workflow/nf_analysis.py

@@ -3,25 +3,18 @@
 import logging
 
 import rich_click as click
-from pydantic import ValidationError
 
 from cg.cli.workflow.commands import ARGUMENT_CASE_ID
 from cg.cli.workflow.utils import validate_force_store_option
-from cg.constants import EXIT_FAIL, EXIT_SUCCESS, Workflow
 from cg.constants.cli_options import COMMENT, DRY_RUN, FORCE
 from cg.constants.constants import MetaApis
-from cg.exc import AnalysisNotReadyError, CgError, HousekeeperStoreError
+from cg.exc import CgError, HousekeeperStoreError
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
 from cg.models.cg_config import CGConfig
-from cg.store.models import Case
 
 LOG = logging.getLogger(__name__)
 
-OPTION_WORKDIR = click.option(
-    "--work-dir",
-    type=click.Path(),
-    help="Directory where intermediate result files are stored",
-)
+
 OPTION_RESUME = click.option(
     "--resume",
     default=True,
@@ -29,205 +22,11 @@ OPTION_RESUME = click.option(
     help="Execute the script using the cached results, useful to continue "
     "executions that were stopped by an error",
 )
-OPTION_PROFILE = click.option(
-    "--profile",
-    type=str,
-    show_default=True,
-    help="Choose a configuration profile",
-)
-
-OPTION_CONFIG = click.option(
-    "--config",
-    type=click.Path(),
-    help="Nextflow config file path",
-)
-
-OPTION_PARAMS_FILE = click.option(
-    "--params-file",
-    type=click.Path(),
-    help="Nextflow workflow-specific parameter file path",
-)
-
-OPTION_USE_NEXTFLOW = click.option(
-    "--use-nextflow",
-    type=bool,
-    is_flag=True,
-    default=False,
-    show_default=True,
-    help="Execute workflow using nextflow",
-)
-
 OPTION_REVISION = click.option(
     "--revision",
     type=str,
     help="Revision of workflow to run (either a git branch, tag or commit SHA number)",
 )
-OPTION_COMPUTE_ENV = click.option(
-    "--compute-env",
-    type=str,
-    help="Compute environment name. If not specified the primary compute environment will be used.",
-)
-OPTION_TOWER_RUN_ID = click.option(
-    "--nf-tower-id",
-    type=str,
-    is_flag=False,
-    default=None,
-    help="NF-Tower ID of run to relaunch. If not provided the latest NF-Tower ID for a case will be used.",
-)
-OPTION_FROM_START = click.option(
-    "--from-start",
-    is_flag=True,
-    default=False,
-    show_default=True,
-    help="Start workflow from start without resuming execution",
-)
-OPTION_STUB = click.option(
-    "--stub-run",
-    is_flag=True,
-    default=False,
-    show_default=True,
-    help="Start a stub workflow",
-)
-
-
-@click.command("config-case")
-@ARGUMENT_CASE_ID
-@DRY_RUN
-@click.pass_obj
-def config_case(context: CGConfig, case_id: str, dry_run: bool) -> None:
-    """Create config files required by a workflow for a case."""
-    analysis_api: NfAnalysisAPI = context.meta_apis[MetaApis.ANALYSIS_API]
-    try:
-        analysis_api.config_case(case_id=case_id, dry_run=dry_run)
-    except (CgError, ValidationError) as error:
-        LOG.error(f"Could not create config files for {case_id}: {error}")
-        raise click.Abort() from error
-
-
-@click.command("run")
-@ARGUMENT_CASE_ID
-@OPTION_WORKDIR
-@OPTION_FROM_START
-@OPTION_PROFILE
-@OPTION_CONFIG
-@OPTION_PARAMS_FILE
-@OPTION_REVISION
-@OPTION_COMPUTE_ENV
-@OPTION_USE_NEXTFLOW
-@OPTION_TOWER_RUN_ID
-@OPTION_STUB
-@DRY_RUN
-@click.pass_obj
-def run(
-    context: CGConfig,
-    case_id: str,
-    work_dir: str,
-    from_start: bool,
-    profile: str,
-    config: str,
-    params_file: str,
-    revision: str,
-    compute_env: str,
-    use_nextflow: bool,
-    nf_tower_id: str | None,
-    stub_run: bool,
-    dry_run: bool,
-) -> None:
-    """Run analysis for a case."""
-    analysis_api: NfAnalysisAPI = context.meta_apis[MetaApis.ANALYSIS_API]
-    try:
-        analysis_api.run_nextflow_analysis(
-            case_id=case_id,
-            dry_run=dry_run,
-            work_dir=work_dir,
-            from_start=from_start,
-            profile=profile,
-            config=config,
-            params_file=params_file,
-            revision=revision,
-            compute_env=compute_env,
-            use_nextflow=use_nextflow,
-            nf_tower_id=nf_tower_id,
-            stub_run=stub_run,
-        )
-    except Exception as error:
-        LOG.error(f"Unspecified error occurred: {error}")
-        raise click.Abort() from error
-
-
-@click.command("start")
-@ARGUMENT_CASE_ID
-@OPTION_WORKDIR
-@OPTION_PROFILE
-@OPTION_CONFIG
-@OPTION_PARAMS_FILE
-@OPTION_REVISION
-@OPTION_COMPUTE_ENV
-@OPTION_USE_NEXTFLOW
-@OPTION_STUB
-@DRY_RUN
-@click.pass_obj
-def start(
-    context: CGConfig,
-    case_id: str,
-    work_dir: str,
-    profile: str,
-    config: str,
-    params_file: str,
-    revision: str,
-    compute_env: str,
-    use_nextflow: bool,
-    stub_run: bool,
-    dry_run: bool,
-) -> None:
-    """Start workflow for a case."""
-    LOG.info(f"Starting analysis for {case_id}")
-    analysis_api: NfAnalysisAPI = context.meta_apis[MetaApis.ANALYSIS_API]
-    try:
-        analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
-        case: Case = analysis_api.status_db.get_case_by_internal_id(case_id)
-        if case.data_analysis != Workflow.NALLO:
-            analysis_api.prepare_fastq_files(case_id=case_id, dry_run=dry_run)
-        analysis_api.config_case(case_id=case_id, dry_run=dry_run)
-        analysis_api.run_nextflow_analysis(
-            case_id=case_id,
-            dry_run=dry_run,
-            work_dir=work_dir,
-            from_start=True,
-            profile=profile,
-            config=config,
-            params_file=params_file,
-            revision=revision,
-            compute_env=compute_env,
-            use_nextflow=use_nextflow,
-            stub_run=stub_run,
-        )
-    except Exception as error:
-        LOG.error(f"Unexpected error occurred: {error}")
-        raise click.Abort from error
-
-
-@click.command("start-available")
-@DRY_RUN
-@click.pass_context
-def start_available(context: click.Context, dry_run: bool = False) -> None:
-    """Start workflow for all cases ready for analysis."""
-    analysis_api: NfAnalysisAPI = context.obj.meta_apis[MetaApis.ANALYSIS_API]
-
-    cases: list[Case] = analysis_api.get_cases_to_analyze()
-    LOG.info(f"Starting {len(cases)} available {analysis_api.workflow} cases")
-
-    exit_code: int = EXIT_SUCCESS
-    for case in cases:
-        try:
-            context.invoke(start, case_id=case.internal_id, dry_run=dry_run)
-        except AnalysisNotReadyError as error:
-            LOG.error(error)
-        except Exception as error:
-            LOG.error(error)
-            exit_code = EXIT_FAIL
-    if exit_code:
-        raise click.Abort
 
 
 @click.command("metrics-deliver")

cg/cli/workflow/raredisease/base.py

@@ -5,22 +5,17 @@ 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, 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,
 )
-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.raredisease import RarediseaseAnalysisAPI
@@ -43,11 +38,7 @@ def raredisease(context: click.Context) -> None:
 
 raredisease.add_command(metrics_deliver)
 raredisease.add_command(resolve_compression)
-raredisease.add_command(config_case)
 raredisease.add_command(report_deliver)
-raredisease.add_command(run)
-raredisease.add_command(start)
-raredisease.add_command(start_available)
 raredisease.add_command(store)
 raredisease.add_command(store_available)
 raredisease.add_command(store_housekeeper)
@@ -56,8 +47,16 @@ raredisease.add_command(store_housekeeper)
 @raredisease.command()
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def dev_config_case(cg_config: CGConfig, case_id: str):
-    """Configure a raredisease case so that it is ready to be run."""
+def config_case(cg_config: CGConfig, case_id: str):
+    """
+    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
+        - CASE_ID_samplesheet.csv
+    """
     factory = ConfiguratorFactory(cg_config)
     configurator = cast(NextflowConfigurator, factory.get_configurator(Workflow.RAREDISEASE))
     configurator.configure(case_id=case_id)
@@ -68,8 +67,16 @@ def dev_config_case(cg_config: CGConfig, case_id: str):
 @OPTION_RESUME
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def dev_run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None):
-    """Run a preconfigured raredisease case."""
+def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None):
+    """
+    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
+        - CASE_ID_samplesheet.csv
+    """
     factory = AnalysisStarterFactory(cg_config)
     analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(
         Workflow.RAREDISEASE
@@ -81,8 +88,17 @@ def dev_run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | Non
 @OPTION_REVISION
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def dev_start(cg_config: CGConfig, case_id: str, revision: str | None):
-    """Start a raredisease case. Configures the case if needed."""
+def start(cg_config: CGConfig, case_id: str, revision: str | None):
+    """
+    Start a raredisease 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)
     analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(
         Workflow.RAREDISEASE
@@ -92,7 +108,7 @@ def dev_start(cg_config: CGConfig, case_id: str, revision: str | None):
 
 @raredisease.command()
 @click.pass_obj
-def dev_start_available(cg_config: CGConfig) -> None:
+def start_available(cg_config: CGConfig) -> None:
     """Starts all available raredisease cases."""
     LOG.info("Starting raredisease workflow for all available cases.")
     analysis_starter = AnalysisStarterFactory(cg_config).get_analysis_starter_for_workflow(
@@ -101,37 +117,3 @@ def dev_start_available(cg_config: CGConfig) -> None:
     succeeded: bool = analysis_starter.start_available()
     if not succeeded:
         raise click.Abort
-
-
-@raredisease.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: RarediseaseAnalysisAPI = 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(case_id=case_id, content=bed_lines)
-
-
-@raredisease.command("managed-variants")
-@DRY_RUN
-@ARGUMENT_CASE_ID
-@click.pass_obj
-def managed_variants(context: CGConfig, case_id: str, dry_run: bool) -> None:
-    """Write managed variants file exported from Scout."""
-
-    analysis_api: RarediseaseAnalysisAPI = context.meta_apis["analysis_api"]
-    analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
-
-    vcf_lines: list[str] = analysis_api.get_managed_variants(case_id=case_id)
-    if dry_run:
-        echo_lines(lines=vcf_lines)
-        return
-    analysis_api.write_managed_variants(case_id=case_id, content=vcf_lines)