cg 76.0.0__py3-none-any.whl → 83.14.0__py3-none-any.whl

cg/cli/workflow/raredisease/base.py

@@ -5,28 +5,25 @@ 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 (
-    config_case,
+    OPTION_RESUME,
+    OPTION_REVISION,
     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
 from cg.models.cg_config import CGConfig
+from cg.services.analysis_starter.analysis_starter import AnalysisStarter
 from cg.services.analysis_starter.configurator.implementations.nextflow import NextflowConfigurator
 from cg.services.analysis_starter.factories.configurator_factory import ConfiguratorFactory
 from cg.services.analysis_starter.factories.starter_factory import AnalysisStarterFactory
-from cg.services.analysis_starter.service import AnalysisStarter
 
 LOG = logging.getLogger(__name__)
 
@@ -41,11 +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)
@@ -54,40 +47,68 @@ 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)
 
 
 @raredisease.command()
+@OPTION_REVISION
+@OPTION_RESUME
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def dev_run(cg_config: CGConfig, case_id: str):
-    """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
     )
-    analysis_starter.run(case_id=case_id)
+    analysis_starter.run(case_id=case_id, resume=resume, revision=revision)
 
 
 @raredisease.command()
+@OPTION_REVISION
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def dev_start(cg_config: CGConfig, case_id: str):
-    """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
     )
-    analysis_starter.start(case_id=case_id)
+    analysis_starter.start(case_id=case_id, revision=revision)
 
 
 @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(
@@ -96,37 +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)

cg/cli/workflow/rnafusion/base.py

@@ -8,6 +8,8 @@ import rich_click as click
 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,
     metrics_deliver,
     report_deliver,
     store,
@@ -18,10 +20,10 @@ from cg.constants.constants import MetaApis, Workflow
 from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.rnafusion import RnafusionAnalysisAPI
 from cg.models.cg_config import CGConfig
+from cg.services.analysis_starter.analysis_starter import AnalysisStarter
 from cg.services.analysis_starter.configurator.implementations.nextflow import NextflowConfigurator
 from cg.services.analysis_starter.factories.configurator_factory import ConfiguratorFactory
 from cg.services.analysis_starter.factories.starter_factory import AnalysisStarterFactory
-from cg.services.analysis_starter.service import AnalysisStarter
 
 LOG = logging.getLogger(__name__)
 
@@ -46,35 +48,63 @@ 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)
 
 
 @rnafusion.command()
+@OPTION_REVISION
+@OPTION_RESUME
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def run(cg_config: CGConfig, case_id: str):
-    """Run a preconfigured RNAFUSION case."""
+def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None):
+    """
+    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
     )
-    analysis_starter.run(case_id=case_id)
+    analysis_starter.run(case_id=case_id, resume=resume, revision=revision)
 
 
 @rnafusion.command()
+@OPTION_REVISION
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def start(cg_config: CGConfig, case_id: str):
-    """Start an RNAFUSION case. Configures the case if needed."""
+def start(cg_config: CGConfig, case_id: str, revision: str | None):
+    """
+    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(
         Workflow.RNAFUSION
     )
-    analysis_starter.start(case_id=case_id)
+    analysis_starter.start(case_id=case_id, revision=revision)
 
 
 @rnafusion.command()

cg/cli/workflow/taxprofiler/base.py

@@ -8,6 +8,8 @@ import rich_click as click
 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,
     metrics_deliver,
     report_deliver,
     store,
@@ -18,10 +20,10 @@ from cg.constants.constants import MetaApis, Workflow
 from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.taxprofiler import TaxprofilerAnalysisAPI
 from cg.models.cg_config import CGConfig
+from cg.services.analysis_starter.analysis_starter import AnalysisStarter
 from cg.services.analysis_starter.configurator.implementations.nextflow import NextflowConfigurator
 from cg.services.analysis_starter.factories.configurator_factory import ConfiguratorFactory
 from cg.services.analysis_starter.factories.starter_factory import AnalysisStarterFactory
-from cg.services.analysis_starter.service import AnalysisStarter
 
 LOG = logging.getLogger(__name__)
 
@@ -35,21 +37,25 @@ def taxprofiler(context: click.Context) -> None:
 
 
 @taxprofiler.command()
+@OPTION_REVISION
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def start(cg_config: CGConfig, case_id: str) -> 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
+def start(cg_config: CGConfig, case_id: str, revision: str | None) -> None:
+    """
+    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)
     analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(
         Workflow.TAXPROFILER
     )
-    analysis_starter.start(case_id=case_id)
+    analysis_starter.start(case_id=case_id, revision=revision)
 
 
 @taxprofiler.command()
@@ -67,30 +73,37 @@ def start_available(cg_config: CGConfig) -> None:
 
 
 @taxprofiler.command()
+@OPTION_REVISION
+@OPTION_RESUME
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def run(cg_config: CGConfig, case_id: str) -> 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
+def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None) -> None:
+    """
+    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)
     analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(
         Workflow.TAXPROFILER
     )
-    analysis_starter.run(case_id=case_id)
+    analysis_starter.run(case_id=case_id, resume=resume, revision=revision)
 
 
 @taxprofiler.command()
 @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/cli/workflow/tomte/base.py

@@ -1,25 +1,29 @@
 """CLI support to create config and/or start Tomte."""
 
 import logging
+from typing import cast
 
 import rich_click as click
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
-from cg.cli.workflow.commands import resolve_compression
+from cg.cli.workflow.commands import ARGUMENT_CASE_ID, resolve_compression
 from cg.cli.workflow.nf_analysis import (
-    config_case,
+    OPTION_RESUME,
+    OPTION_REVISION,
     metrics_deliver,
     report_deliver,
-    run,
-    start,
-    start_available,
     store,
     store_available,
     store_housekeeper,
 )
-from cg.constants.constants import MetaApis
+from cg.constants.constants import MetaApis, Workflow
 from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.tomte import TomteAnalysisAPI
+from cg.models.cg_config import CGConfig
+from cg.services.analysis_starter.analysis_starter import AnalysisStarter
+from cg.services.analysis_starter.configurator.implementations.nextflow import NextflowConfigurator
+from cg.services.analysis_starter.factories.configurator_factory import ConfiguratorFactory
+from cg.services.analysis_starter.factories.starter_factory import AnalysisStarterFactory
 
 LOG = logging.getLogger(__name__)
 
@@ -33,12 +37,81 @@ 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)
 tomte.add_command(store)
 tomte.add_command(store_available)
+
+
+@tomte.command("config-case")
+@ARGUMENT_CASE_ID
+@click.pass_obj
+def config_case(cg_config: CGConfig, case_id: str):
+    """
+    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
+        - CASE_ID_samplesheet.csv
+        - gene_panels.bed
+    """
+    factory = ConfiguratorFactory(cg_config)
+    configurator = cast(NextflowConfigurator, factory.get_configurator(Workflow.TOMTE))
+    configurator.configure(case_id=case_id)
+
+
+@tomte.command("run")
+@OPTION_REVISION
+@OPTION_RESUME
+@ARGUMENT_CASE_ID
+@click.pass_obj
+def run(cg_config: CGConfig, case_id: str, resume: bool, revision: str | None) -> None:
+    """
+    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
+        - CASE_ID_samplesheet.csv
+        - gene_panels.bed
+    """
+    factory = AnalysisStarterFactory(cg_config)
+    analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(Workflow.TOMTE)
+    analysis_starter.run(case_id=case_id, resume=resume, revision=revision)
+
+
+@tomte.command("start")
+@OPTION_REVISION
+@ARGUMENT_CASE_ID
+@click.pass_obj
+def start(cg_config: CGConfig, case_id: str, revision: str | None):
+    """
+    Start a Tomte case.
+
+    \b
+    Configures the case and writes the following files:
+        - CASE_ID_params_file.yaml
+        - CASE_ID_nextflow_config.json
+        - CASE_ID_samplesheet.csv
+        - gene_panels.bed
+    and submits the job to the Seqera Platform.
+    """
+    factory = AnalysisStarterFactory(cg_config)
+    analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(Workflow.TOMTE)
+    analysis_starter.start(case_id=case_id, revision=revision)
+
+
+@tomte.command("start-available")
+@click.pass_obj
+def start_available(cg_config: CGConfig):
+    """Starts all available Tomte cases."""
+    LOG.info("Starting Tomte workflow for all available cases.")
+    factory = AnalysisStarterFactory(cg_config)
+    analysis_starter: AnalysisStarter = factory.get_analysis_starter_for_workflow(Workflow.TOMTE)
+    succeeded: bool = analysis_starter.start_available()
+    if not succeeded:
+        raise click.Abort

cg/constants/constants.py

@@ -60,20 +60,23 @@ DEFAULT_CAPTURE_KIT = "twistexomecomprehensive_10.2_hg19_design.bed"
 
 
 class CustomerId(StrEnum):
-    CG_INTERNAL_CUSTOMER: str = "cust000"
-    CUST001: str = "cust001"
-    CUST002: str = "cust002"
-    CUST003: str = "cust003"
-    CUST004: str = "cust004"
-    CUST032: str = "cust032"
-    CUST042: str = "cust042"
-    CUST110: str = "cust110"
-    CUST127: str = "cust127"
-    CUST132: str = "cust132"
-    CUST143: str = "cust143"
-    CUST147: str = "cust147"
-    CUST201: str = "cust201"
-    CUST999: str = "cust999"
+    CG_INTERNAL_CUSTOMER = "cust000"
+    CUST001 = "cust001"
+    CUST002 = "cust002"
+    CUST003 = "cust003"
+    CUST004 = "cust004"
+    CUST032 = "cust032"
+    CUST042 = "cust042"
+    CUST087 = "cust087"
+    CUST110 = "cust110"
+    CUST127 = "cust127"
+    CUST132 = "cust132"
+    CUST143 = "cust143"
+    CUST147 = "cust147"
+    CUST175 = "cust175"
+    CUST185 = "cust185"
+    CUST201 = "cust201"
+    CUST999 = "cust999"
 
 
 class SequencingRunDataAvailability(StrEnum):
@@ -97,9 +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}$"
@@ -153,12 +156,12 @@ class FileFormat(StrEnum):
 
 
 class GenomeVersion(StrEnum):
-    GRCh37: str = "GRCh37"
-    GRCh38: str = "GRCh38"
-    T2T_CHM13: str = "T2T-CHM13v2.0"
+    GRCh37 = "GRCh37"
+    GRCh38 = "GRCh38"
+    T2T_CHM13 = "T2T-CHM13v2.0"
     CANFAM3 = auto()
-    HG19: str = "hg19"
-    HG38: str = "hg38"
+    HG19 = "hg19"
+    HG38 = "hg38"
 
 
 class SampleType(StrEnum):
@@ -235,7 +238,6 @@ class APIMethods(StrEnum):
 
 class MicrosaltQC:
     AVERAGE_COVERAGE_THRESHOLD: int = 10
-    MWX_THRESHOLD_SAMPLES_PASSING: float = 0.9
     COVERAGE_10X_THRESHOLD: float = 0.75
     DUPLICATION_RATE_THRESHOLD: float = 0.8
     INSERT_SIZE_THRESHOLD: int = 100
@@ -245,13 +247,6 @@ class MicrosaltQC:
     TARGET_READS_FAIL_THRESHOLD: float = 0.7
 
 
-class MicrosaltAppTags(StrEnum):
-    MWRNXTR003: str = "MWRNXTR003"
-    MWXNXTR003: str = "MWXNXTR003"
-    VWGNXTR001: str = "VWGNXTR001"
-    PREP_CATEGORY: str = "mic"
-
-
 class MutantQC:
     EXTERNAL_NEGATIVE_CONTROL_READS_THRESHOLD: int = 100000
     INTERNAL_NEGATIVE_CONTROL_READS_THRESHOLD: int = 2000

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/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"
@@ -35,6 +36,7 @@ class GenePanelMasterList(StrEnum):
     MTDNA = "mtDNA"
     NBS_M = "NBS-M"
     NEURODEG = "NEURODEG"
+    NOONAN = "NOONAN"
     NMD = "NMD"
     OMIM_AUTO = "OMIM-AUTO"
     OPTIC = "OPTIC"
@@ -47,7 +49,7 @@ class GenePanelMasterList(StrEnum):
     SOVM = "SOVM"
     STROKE = "STROKE"
     AID = "AID"
-    INHERITED_CANCER = "Inherited cancer"
+    IHC = "IHC"
     VEO_IBD = "VEO-IBD"
     KIDNEY = "Kidney"
     CAKUT = "CAKUT"

cg/constants/housekeeper_tags.py

@@ -57,34 +57,34 @@ class HermesFileTag(StrEnum):
 class AnalysisTag(StrEnum):
     """Tags for analysis files."""
 
-    ARRIBA: str = "arriba"
-    ARRIBA_VISUALIZATION: str = "arriba-visualisation"
-    BED: str = "bed"
-    BIGWIG: str = "bigwig"
-    CLINICAL: str = "clinical"
-    COVERAGE: str = "coverage"
-    FRASER: str = "fraser"
-    FUSION: str = "fusion"
-    FUSIONCATCHER: str = "fusioncatcher"
-    FUSIONCATCHER_SUMMARY: str = "fusioncatcher-summary"
-    FUSIONINSPECTOR: str = "fusioninspector"
-    FUSIONINSPECTOR_HTML: str = "fusioninspector-html"
-    FUSIONREPORT: str = "fusionreport"
-    GENE_COUNTS: str = "gene-counts"
-    JUNCTION: str = "junction"
-    MULTIQC_HTML: str = "multiqc-html"
-    OUTRIDER: str = "outrider"
-    REPEATS: str = "repeats"
-    RESEARCH: str = "research"
-    RNA: str = "rna"
-    SMN_CALLING: str = "smn-calling"
-    STARFUSION: str = "star-fusion"
-    VCF_FUSION: str = "vcf-fusion"
-    VCF_SNV: str = "vcf-snv"
-    VCF_SNV_CLINICAL: str = "vcf-snv-clinical"
-    VCF_STR: str = "vcf-str"
-    VCF_SV_CLINICAL: str = "vcf-sv-clinical"
-    VCF_SV: str = "vcf-sv"
+    ARRIBA = "arriba"
+    ARRIBA_VISUALIZATION = "arriba-visualisation"
+    BED = "bed"
+    BIGWIG = "bigwig"
+    CLINICAL = "clinical"
+    COVERAGE = "coverage"
+    FRASER = "fraser"
+    FUSION = "fusion"
+    FUSIONCATCHER = "fusioncatcher"
+    FUSIONCATCHER_SUMMARY = "fusioncatcher-summary"
+    FUSIONINSPECTOR = "fusioninspector"
+    FUSIONINSPECTOR_HTML = "fusioninspector-html"
+    FUSIONREPORT = "fusionreport"
+    GENE_COUNTS = "gene-counts"
+    JUNCTION = "junction"
+    MULTIQC_HTML = "multiqc-html"
+    OUTRIDER = "outrider"
+    REPEATS = "repeats"
+    RESEARCH = "research"
+    RNA = "rna"
+    SMN_CALLING = "smn-calling"
+    STARFUSION = "star-fusion"
+    VCF_FUSION = "vcf-fusion"
+    VCF_SNV = "vcf-snv"
+    VCF_SNV_CLINICAL = "vcf-snv-clinical"
+    VCF_STR = "vcf-str"
+    VCF_SV_CLINICAL = "vcf-sv-clinical"
+    VCF_SV = "vcf-sv"
 
 
 class HkMipAnalysisTag:

cg/constants/lims.py

@@ -145,6 +145,10 @@ MASTER_STEPS_UDFS = {
             "atlas_document": "Sequencing Method",
             "atlas_version": "Atlas Version",
         },
+        "Set Up Sequencing Run (Revio) v2": {
+            "atlas_document": "Sequencing Method",
+            "atlas_version": "Atlas Version",
+        },
     },
     "delivery_method_step": {
         "CG002 - Delivery": {