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

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/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/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/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/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/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": {

cg/constants/orderforms.py

@@ -31,7 +31,7 @@ class Orderform(StrEnum):
         """Returns the current version of the given order form."""
         current_order_form_versions = {
             Orderform.MIP_DNA: "35",
-            Orderform.RML: "20",
+            Orderform.RML: "21",
             Orderform.MICROSALT: "12",
             Orderform.NALLO: "1",
             Orderform.SARS_COV_2: "10",

cg/constants/pacbio.py

@@ -64,6 +64,7 @@ class SmrtLinkDatabasesAliases:
     BIO_SAMPLE_NAME: str = "bioSampleName"
     CELL_ID: str = "cellId"
     CELL_INDEX: str = "cellIndex"
+    INSTRUMENT_NAME: str = "instrumentName"
     MOVIE_NAME: str = "metadataContextId"
     PATH: str = "path"
     RUN_COMPLETED_AT = "createdAt"

cg/constants/scout.py

@@ -66,12 +66,12 @@ NALLO_CASE_TAGS = dict(
     multiqc={"multiqc-html"},
     peddy_check={"ped-check", "peddy"},
     peddy_ped={"ped", "peddy"},
-    peddy_sex={"sex-check", "peddy"},
-    vcf_snv_research={"vcf-snv-research"},
+    somalier_samples={"somalier", "relate-samples"},
     vcf_snv={"vcf-snv-clinical"},
-    vcf_sv_research={"vcf-sv-research"},
-    vcf_sv={"vcf-sv-clinical"},
+    vcf_snv_research={"vcf-snv-research"},
     vcf_str={"vcf-str"},
+    vcf_sv={"vcf-sv-clinical"},
+    vcf_sv_research={"vcf-sv-research"},
 )
 
 MIP_CASE_TAGS: dict[str, set[str]] = dict(
@@ -138,6 +138,8 @@ RAREDISEASE_SAMPLE_TAGS: dict[str, set[str]] = dict(
 NALLO_SAMPLE_TAGS: dict[str, set[str]] = dict(
     alignment_path={AlignmentFileTag.BAM, "haplotags"},
     assembly_alignment_path={AlignmentFileTag.BAM, "assembly"},
+    chromograph_autozyg={"chromograph", "autozyg"},
+    chromograph_coverage={"chromograph", "tcov"},
     d4_file={"coverage", "d4"},
     hificnv_coverage={"hificnv", "bigwig"},
     paraphase_alignment_path={AlignmentFileTag.BAM, NalloAnalysisTag.PARAPHASE},

cg/exc.py

@@ -150,6 +150,14 @@ class IlluminaRunAlreadyBackedUpError(CgError):
     """Raised when a flow cell is already backed-up."""
 
 
+class PacbioSequencingRunAlreadyExistsError(CgError):
+    """Raised when a PacBio sequencing run already exists."""
+
+
+class PacbioSequencingRunNotFoundError(CgError):
+    """Raised when a PacBio sequencing run is not found."""
+
+
 class HousekeeperFileMissingError(CgError):
     """
     Exception raised when a file is missing in Housekeeper.
@@ -216,10 +224,6 @@ class RunParametersError(CgError):
     """Raised when something is wrong with the run parameters file."""
 
 
-class NfSampleSheetError(CgError):
-    """Raised when something is wrong with the sample sheet."""
-
-
 class SampleSheetContentError(CgError):
     """Raised when something is wrong with the sample sheet content."""
 
@@ -350,3 +354,7 @@ class MissingConfigFilesError(CgError):
 
 class SeqeraError(CgError):
     """Exception raised when receiving an unexpected response from Seqera platform"""
+
+
+class ApplicationDoesNotHaveHiFiYieldError(CgError):
+    """Exception raised when application does not have HiFi yield set."""

cg/meta/compress/compress.py

@@ -96,8 +96,13 @@ class CompressAPI:
     def decompress_case(self, case: Case) -> None:
         """Decompresses all Spring files tied to the case.
         Raises:
-            DecompressionFailedToStartError if no sample could start decompressing."""
-        if not any(self.decompress_spring(sample.internal_id) for sample in case.samples):
+            DecompressionCouldNotStartError if no sample could start decompressing.
+        """
+        success = False
+        for sample in case.samples:
+            if self.decompress_spring(sample.internal_id):
+                success = True
+        if not success:
             raise DecompressionCouldNotStartError(
                 f"No sample could be decompressed for {case.internal_id}"
             )

cg/meta/delivery_report/nallo.py

@@ -52,7 +52,7 @@ class NalloDeliveryReportAPI(DeliveryReportAPI):
             median_coverage=sample_metrics.median_coverage,
             million_read_pairs=get_million_read_pairs(sample.reads),
             pct_10x=coverage_metrics.coverage_completeness_percent if coverage_metrics else None,
-            sex=sample_metrics.predicted_sex_sex_check,
+            sex=sample_metrics.predicted_sex,
         )
 
     def is_report_accredited(

cg/meta/delivery_report/templates/macros/ticket_system.html

@@ -2,7 +2,7 @@
   <div class="container">
     <div class="alert alert-info" role="alert">
       All kommunikation gällande ordern, såsom tillägg, avvikelser eller ev undantag i metoden från
-      Clinical Genomics, finns tillgänglig i SupportSystem och är länkad till ärendets ticket:
+      Clinical Genomics, finns tillgänglig i Freshdesk och är länkad till ärendets ticket:
       <a class="alert-link">#{{ ticket_id }}</a>. En stängd ticket kan närsomhelst öppnas upp igen för frågor.
     </div>
   </div>

cg/meta/observations/balsamic_observations_api.py

@@ -82,7 +82,7 @@ class BalsamicObservationsAPI(ObservationsAPI):
             [
                 self.is_customer_eligible_for_observations_upload(case.customer.internal_id),
                 self.is_analysis_type_eligible_for_observations_upload(case),
-                self.is_sample_source_type_ffpe(case.internal_id),
+                self.is_sample_source_type_not_ffpe(case.internal_id),
                 self.is_panel_allowed_for_observations_upload(case),
             ]
         )

cg/meta/observations/mip_dna_observations_api.py

@@ -58,7 +58,7 @@ class MipDNAObservationsAPI(ObservationsAPI):
                 self.is_customer_eligible_for_observations_upload(case.customer.internal_id),
                 self.is_sequencing_method_eligible_for_observations_upload(case.internal_id),
                 self.is_sample_type_eligible_for_observations_upload(case),
-                self.is_sample_source_type_ffpe(case.internal_id),
+                self.is_sample_source_type_not_ffpe(case.internal_id),
             ]
         )
 

cg/meta/observations/nallo_observations_api.py

@@ -59,7 +59,7 @@ class NalloObservationsAPI(ObservationsAPI):
                 self.is_customer_eligible_for_observations_upload(case.customer.internal_id),
                 self.is_sequencing_method_eligible_for_observations_upload(case.internal_id),
                 self.is_sample_type_eligible_for_observations_upload(case),
-                self.is_sample_source_type_ffpe(case.internal_id),
+                self.is_sample_source_type_not_ffpe(case.internal_id),
             ]
         )
 

cg/meta/observations/observations_api.py

@@ -132,7 +132,7 @@ class ObservationsAPI:
             return False
         return True
 
-    def is_sample_source_type_ffpe(self, case_id: str) -> bool:
+    def is_sample_source_type_not_ffpe(self, case_id: str) -> bool:
         source_type: str | None = self.analysis_api.get_case_source_type(case_id)
         if source_type and SourceType.FFPE.lower() not in source_type.lower():
             return True

cg/meta/observations/raredisease_observations_api.py

@@ -58,7 +58,7 @@ class RarediseaseObservationsAPI(ObservationsAPI):
                 self.is_customer_eligible_for_observations_upload(case.customer.internal_id),
                 self.is_sequencing_method_eligible_for_observations_upload(case.internal_id),
                 self.is_sample_type_eligible_for_observations_upload(case),
-                self.is_sample_source_type_ffpe(case.internal_id),
+                self.is_sample_source_type_not_ffpe(case.internal_id),
             ]
         )
 

cg/meta/tar/tar.py

@@ -24,8 +24,9 @@ class TarAPI:
         self.process.run_command(command, dry_run=self.dry_run)
 
     @staticmethod
-    def get_extract_file_command(input_file: Path, output_dir: Path) -> list[str]:
-        """Generates the Tar command for flow cel run directory extraction"""
+    def get_extract_file_command(input_file: Path, output_dir: Path, is_current: bool) -> list[str]:
+        """Generates the Tar command for flow cel run directory extraction. If the is_current flag
+        is set, the command will strip the first 6 components of the file path when extracting."""
         extraction_parameters: list = FlowCellExtractionParameters.EXTRACT_FILE.copy()
         extraction_parameters.append(str(input_file))
         exclude_files: list = FlowCellExtractionParameters.EXCLUDE_FILES.copy()
@@ -33,6 +34,8 @@ class TarAPI:
         target_directory_parameters: list = FlowCellExtractionParameters.CHANGE_TO_DIR.copy()
         extraction_parameters.extend(target_directory_parameters)
         extraction_parameters.append(str(output_dir))
+        if is_current:
+            extraction_parameters.append("--strip-components=6")
         return extraction_parameters
 
     def get_compress_cmd(self, input_path: Path) -> str:

cg/meta/upload/coverage.py

@@ -25,15 +25,15 @@ class UploadCoverageApi:
         """Get data for uploading coverage."""
         case_id = analysis.case.internal_id
         data = {"family": case_id, "family_name": analysis.case.name, "samples": []}
-        for link_obj in analysis.case.links:
+        for sample in analysis.case.samples:
             hk_coverage: File = self.hk_api.files(
                 version=analysis.housekeeper_version_id,
-                tags=[link_obj.sample.internal_id, "coverage"],
-            ).first()
+                tags={sample.internal_id, "coverage", "sambamba-depth", "chanjo"},
+            ).one()
             data["samples"].append(
                 {
-                    "sample": link_obj.sample.internal_id,
-                    "sample_name": link_obj.sample.name,
+                    "sample": sample.internal_id,
+                    "sample_name": sample.name,
                     "coverage": hk_coverage.full_path,
                 }
             )

cg/meta/upload/raredisease/raredisease.py

@@ -6,6 +6,7 @@ import logging
 import rich_click as click
 
 from cg.cli.generate.delivery_report.base import generate_delivery_report
+from cg.cli.upload.coverage import upload_coverage
 from cg.cli.upload.genotype import upload_genotypes
 from cg.cli.upload.gens import upload_to_gens
 from cg.cli.upload.observations import upload_observations_to_loqusdb
@@ -31,6 +32,8 @@ class RarediseaseUploadAPI(UploadAPI):
         analysis: Analysis = self.status_db.get_latest_completed_analysis_for_case(case.internal_id)
         self.update_upload_started_at(analysis=analysis)
 
+        ctx.invoke(upload_coverage, family_id=case.internal_id)
+
         # Delivery report generation
         if case.data_delivery in REPORT_SUPPORTED_DATA_DELIVERY:
             ctx.invoke(generate_delivery_report, case_id=case.internal_id)

cg/meta/upload/scout/nallo_config_builder.py

@@ -90,6 +90,20 @@ class NalloConfigBuilder(ScoutConfigBuilder):
         """Include sample level files that are optional."""
         LOG.info("Including NALLO specific sample level files")
         sample_id: str = cast(str, config_sample.sample_id)
+        config_sample.chromograph_images.autozygous = self.remove_chromosome_substring(
+            self.get_sample_file(
+                hk_tags=self.sample_tags.chromograph_autozyg,
+                sample_id=sample_id,
+                hk_version=hk_version,
+            )
+        )
+        config_sample.chromograph_images.coverage = self.remove_chromosome_substring(
+            self.get_sample_file(
+                hk_tags=self.sample_tags.chromograph_coverage,
+                sample_id=sample_id,
+                hk_version=hk_version,
+            )
+        )
         config_sample.d4_file = self.get_sample_file(
             hk_tags=cast(set[str], self.sample_tags.d4_file),
             sample_id=sample_id,