Merge branch 'master' into delete-flowcell-post-processing

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 53.5.4
+current_version = 53.6.0
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "53.5.4"
+__version__ = "53.6.0"

cg/cli/workflow/mip/base.py

@@ -51,13 +51,13 @@ def config_case(context: CGConfig, case_id: str, panel_bed: str, dry_run: bool):
 @OPTION_DRY
 @ARGUMENT_CASE_ID
 @click.pass_obj
-def panel(context: CGConfig, case_id: str, dry_run: bool):
+def panel(context: CGConfig, case_id: str, dry_run: bool) -> None:
     """Write aggregated gene panel file exported from Scout."""
 
     analysis_api: MipAnalysisAPI = context.meta_apis["analysis_api"]
     analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
 
-    bed_lines: list[str] = analysis_api.panel(case_id=case_id)
+    bed_lines: list[str] = analysis_api.get_gene_panel(case_id=case_id)
     if dry_run:
         for bed_line in bed_lines:
             click.echo(bed_line)

cg/cli/workflow/mip_dna/base.py

@@ -1,4 +1,4 @@
-"""Commands to start MIP rare disease DNA workflow"""
+"""Commands to start MIP rare disease DNA workflow."""
 
 import logging
 

cg/cli/workflow/raredisease/base.py

@@ -4,18 +4,38 @@
 
 import click
 
+from cg.cli.workflow.commands import ARGUMENT_CASE_ID, OPTION_DRY
 from cg.constants.constants import MetaApis
 from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.raredisease import RarediseaseAnalysisAPI
+from cg.models.cg_config import CGConfig
 
 LOG = logging.getLogger(__name__)
 
 
 @click.group(invoke_without_command=True)
 @click.pass_context
 def raredisease(context: click.Context) -> None:
-    """nf-core/raredisease analysis workflow."""
+    """NF-core/raredisease analysis workflow."""
     AnalysisAPI.get_help(context)
     context.obj.meta_apis[MetaApis.ANALYSIS_API] = RarediseaseAnalysisAPI(
         config=context.obj,
     )
+
+
+@raredisease.command("panel")
+@OPTION_DRY
+@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:
+        for bed_line in bed_lines:
+            click.echo(bed_line)
+        return
+    analysis_api.write_panel(case_id=case_id, content=bed_lines)

cg/constants/__init__.py

@@ -8,8 +8,6 @@
 from cg.constants.constants import (
     CAPTUREKIT_CANCER_OPTIONS,
     CAPTUREKIT_OPTIONS,
-    COLLABORATORS,
-    COMBOS,
     CONTAINER_OPTIONS,
     DEFAULT_CAPTURE_KIT,
     PREP_CATEGORIES,

cg/constants/constants.py

@@ -43,31 +43,25 @@ def actions(cls) -> list[str]:
         return list(cls)
 
 
-COLLABORATORS = ("cust000", "cust002", "cust003", "cust004", "cust042")
-
-COMBOS = {
-    "DSD": ("DSD", "DSD-S", "HYP", "SEXDIF", "SEXDET"),
-    "CM": ("CNM", "CM"),
-    "Horsel": ("Horsel", "141217", "141201"),
-    "OPHTHALMO": (
-        "OPHTHALMO",
-        "ANTE-ED",
-        "CATARACT",
-        "CORNEA",
-        "GLAUCOMA",
-        "RETINA",
-        "SED",
-        "ALBINISM",
-    ),
-}
-
 CONTAINER_OPTIONS = ("Tube", "96 well plate", "No container")
 
 CONTROL_OPTIONS = ("", "negative", "positive")
 
 DEFAULT_CAPTURE_KIT = "twistexomerefseq_9.1_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"
+    CUST132: str = "cust132"
+    CUST999: str = "cust999"
+
+
 class FlowCellStatus(StrEnum):
     ON_DISK: str = "ondisk"
     REMOVED: str = "removed"

cg/constants/gene_panel.py

@@ -3,6 +3,8 @@
 
 from enum import StrEnum
 
+from cg.constants.constants import CustomerId
+
 GENOME_BUILD_37: str = "37"
 GENOME_BUILD_38: str = "GRCh38"
 
@@ -44,3 +46,32 @@ class GenePanelMasterList(StrEnum):
     def get_panel_names(cls, panels=None) -> list[str]:
         """Return requested panel names from the Master list, or all panels if none are specified."""
         return list(panels) if panels else list(cls)
+
+    @staticmethod
+    def collaborators() -> set[str]:
+        """Return collaborators of the Master list."""
+        return {
+            CustomerId.CG_INTERNAL_CUSTOMER,
+            CustomerId.CUST002,
+            CustomerId.CUST003,
+            CustomerId.CUST004,
+            CustomerId.CUST042,
+        }
+
+
+class GenePanelCombo:
+    COMBO_1: dict[str, set[str]] = {
+        "DSD": {"DSD", "DSD-S", "HYP", "SEXDIF", "SEXDET"},
+        "CM": {"CNM", "CM"},
+        "Horsel": {"Horsel", "141217", "141201"},
+        "OPHTHALMO": (
+            "OPHTHALMO",
+            "ANTE-ED",
+            "CATARACT",
+            "CORNEA",
+            "GLAUCOMA",
+            "RETINA",
+            "SED",
+            "ALBINISM",
+        ),
+    }

cg/constants/invoice.py

@@ -1,14 +1,6 @@
 from enum import StrEnum
 
 
-class CustomerNames(StrEnum):
-    cust999: str = "cust999"
-    cust032: str = "cust032"
-    cust001: str = "cust001"
-    cust132: str = "cust132"
-    CG_INTERNAL_CUSTOMER: str = "cust000"
-
-
 class CostCenters(StrEnum):
     ki: str = "ki"
     kth: str = "kth"

cg/io/controller.py

@@ -7,7 +7,7 @@
 from cg.io.api import delete, get, patch, post, put
 from cg.io.csv import read_csv, read_csv_stream, write_csv, write_csv_stream
 from cg.io.json import read_json, read_json_stream, write_json, write_json_stream
-from cg.io.txt import read_txt
+from cg.io.txt import read_txt, write_txt
 from cg.io.xml import read_xml, write_xml
 from cg.io.yaml import read_yaml, read_yaml_stream, write_yaml, write_yaml_stream
 
@@ -50,6 +50,7 @@ class WriteFile:
     write_file = {
         FileFormat.CSV: write_csv,
         FileFormat.JSON: write_json,
+        FileFormat.TXT: write_txt,
         FileFormat.YAML: write_yaml,
         FileFormat.XML: write_xml,
     }

cg/io/txt.py

@@ -9,3 +9,9 @@ def read_txt(file_path: Path, read_to_string: bool = False) -> list[str] | str:
         if read_to_string:
             return file.read()
         return list(file)
+
+
+def write_txt(content: list[str], file_path: Path) -> None:
+    """Write content to a text file."""
+    with open(file_path, "w") as file:
+        file.writelines(content)

cg/meta/invoice.py

@@ -3,7 +3,8 @@
 from pydantic.v1 import ValidationError
 
 from cg.apps.lims import LimsAPI
-from cg.constants.invoice import CostCenters, CustomerNames
+from cg.constants.constants import CustomerId
+from cg.constants.invoice import CostCenters
 from cg.constants.priority import PriorityTerms
 from cg.constants.sequencing import RecordType
 from cg.models.invoice.invoice import (
@@ -44,7 +45,7 @@ def _set_record_type(self):
     def get_customer_by_cost_center(self, cost_center: str) -> Customer | str:
         """Return the costumer based on cost center."""
         return (
-            self.db.get_customer_by_internal_id(customer_internal_id=CustomerNames.cust999)
+            self.db.get_customer_by_internal_id(customer_internal_id=CustomerId.CUST999)
             if cost_center.lower() == CostCenters.kth
             else self.customer_obj
         )
@@ -212,7 +213,7 @@ def get_lims_id(self, record: Sample or Pool) -> str:
 
     def get_priority(self, record: Sample or Pool, for_discount_price: bool = False) -> str:
         """Return the priority."""
-        if self.customer_obj.internal_id == CustomerNames.cust032:
+        if self.customer_obj.internal_id == CustomerId.CUST032:
             priority = PriorityTerms.STANDARD
         elif self.record_type == RecordType.Pool or (
             record.priority_human == "clinical trials" and for_discount_price

cg/meta/orders/fastq_submitter.py

@@ -1,15 +1,14 @@
 import datetime as dt
 
 from cg.constants import DataDelivery, GenePanelMasterList
-from cg.constants.constants import Pipeline, PrepCategory
-from cg.constants.invoice import CustomerNames
+from cg.constants.constants import CustomerId, Pipeline, PrepCategory
 from cg.constants.priority import Priority
 from cg.exc import OrderError
 from cg.meta.orders.lims import process_lims
 from cg.meta.orders.submitter import Submitter
 from cg.models.orders.order import OrderIn
 from cg.models.orders.sample_base import StatusEnum
-from cg.store.models import ApplicationVersion, Customer, Case, CaseSample, Sample
+from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Sample
 
 
 class FastqSubmitter(Submitter):
@@ -66,7 +65,7 @@ def create_maf_case(self, sample_obj: Sample) -> None:
             ticket=sample_obj.original_ticket,
         )
         case.customer = self.status.get_customer_by_internal_id(
-            customer_internal_id=CustomerNames.CG_INTERNAL_CUSTOMER
+            customer_internal_id=CustomerId.CG_INTERNAL_CUSTOMER
         )
         relationship: CaseSample = self.status.relate_sample(
             case=case, sample=sample_obj, status=StatusEnum.unknown

cg/meta/upload/scout/mip_config_builder.py

@@ -56,9 +56,10 @@ def build_load_config(self, rank_score_threshold: int = 5) -> None:
         self.load_config.rank_model_version = mip_analysis_data.rank_model_version
         self.load_config.sv_rank_model_version = mip_analysis_data.sv_rank_model_version
 
-        self.load_config.gene_panels = (
-            self.mip_analysis_api.convert_panels(
-                self.analysis_obj.case.customer.internal_id, self.analysis_obj.case.panels
+        self.load_config.gene_panels: list[str] | None = (
+            self.mip_analysis_api.get_aggregated_panels(
+                customer_id=self.analysis_obj.case.customer.internal_id,
+                default_panels=set(self.analysis_obj.case.panels),
             )
             or None
         )

cg/meta/workflow/analysis.py

@@ -11,6 +11,7 @@
 from cg.apps.environ import environ_email
 from cg.constants import EXIT_FAIL, EXIT_SUCCESS, Pipeline, Priority
 from cg.constants.constants import AnalysisType, CaseActions, WorkflowManager
+from cg.constants.gene_panel import GenePanelCombo
 from cg.exc import AnalysisNotReadyError, BundleAlreadyAddedError, CgDataError, CgError
 from cg.meta.meta import MetaAPI
 from cg.meta.workflow.fastq import FastqHandler
@@ -21,6 +22,15 @@
 LOG = logging.getLogger(__name__)
 
 
+def add_gene_panel_combo(default_panels: set[str]) -> set[str]:
+    """Add gene panels combinations for gene panels being part of gene panel combination and return updated gene panels."""
+    all_panels = default_panels
+    for panel in default_panels:
+        if panel in GenePanelCombo.COMBO_1:
+            all_panels |= GenePanelCombo.COMBO_1.get(panel)
+    return all_panels
+
+
 class AnalysisAPI(MetaAPI):
     """
     Parent class containing all methods that are either shared or overridden by other workflow APIs
@@ -498,3 +508,11 @@ def prepare_fastq_files(self, case_id: str, dry_run: bool) -> None:
         self.resolve_decompression(case_id, dry_run=dry_run)
         if not self.is_case_ready_for_analysis(case_id):
             raise AnalysisNotReadyError("FASTQ file are not present for the analysis to start")
+
+    def _get_gene_panel(self, case_id: str, genome_build: str) -> list[str]:
+        """Create and return the aggregated gene panel file."""
+        case: Case = self.status_db.get_case_by_internal_id(internal_id=case_id)
+        all_panels: list[str] = self.get_aggregated_panels(
+            customer_id=case.customer.internal_id, default_panels=set(case.panels)
+        )
+        return self.scout_api.export_panels(build=genome_build, panels=all_panels)

cg/meta/workflow/mip.py

@@ -5,18 +5,12 @@
 from pydantic.v1 import ValidationError
 
 from cg.apps.mip.confighandler import ConfigHandler
-from cg.constants import (
-    COLLABORATORS,
-    COMBOS,
-    FileExtensions,
-    GenePanelMasterList,
-    Pipeline,
-)
+from cg.constants import FileExtensions, GenePanelMasterList, Pipeline
 from cg.constants.constants import FileFormat
 from cg.constants.housekeeper_tags import HkMipAnalysisTag
 from cg.exc import CgError
 from cg.io.controller import ReadFile, WriteFile
-from cg.meta.workflow.analysis import AnalysisAPI
+from cg.meta.workflow.analysis import AnalysisAPI, add_gene_panel_combo
 from cg.meta.workflow.fastq import MipFastqHandler
 from cg.models.cg_config import CGConfig
 from cg.models.mip.mip_analysis import MipAnalysis
@@ -156,36 +150,29 @@ def link_fastq_files(self, case_id: str, dry_run: bool = False) -> None:
                 sample_obj=link.sample,
             )
 
-    def write_panel(self, case_id: str, content: list[str]):
-        """Write the gene panel to case dir"""
+    def write_panel(self, case_id: str, content: list[str]) -> None:
+        """Write the gene panel to case dir."""
         out_dir = Path(self.root, case_id)
         out_dir.mkdir(parents=True, exist_ok=True)
-        out_path = Path(out_dir, "gene_panels.bed")
-        with out_path.open("w") as out_handle:
-            out_handle.write("\n".join(content))
+        WriteFile.write_file_from_content(
+            content="\n".join(content),
+            file_format=FileFormat.TXT,
+            file_path=Path(out_dir, f"gene_panels{FileExtensions.BED}"),
+        )
 
     @staticmethod
-    def convert_panels(customer: str, default_panels: list[str]) -> list[str]:
-        """Convert between default panels and all panels included in gene list."""
-        # check if all default panels are part of master list
+    def get_aggregated_panels(customer_id: str, default_panels: set[str]) -> list[str]:
+        """Check if customer should use the gene panel master list
+        and if all default panels are included in the gene panel master list.
+        If not, add gene panel combo and OMIM-AUTO.
+        Return an aggregated gene panel."""
         master_list: list[str] = GenePanelMasterList.get_panel_names()
-        if customer in COLLABORATORS and set(default_panels).issubset(master_list):
+        if customer_id in GenePanelMasterList.collaborators() and default_panels.issubset(
+            master_list
+        ):
             return master_list
-
-        # the rest are handled the same way
-        all_panels = set(default_panels)
-
-        # fill in extra panels if selection is part of a combo
-        for panel in default_panels:
-            if panel in COMBOS:
-                for extra_panel in COMBOS[panel]:
-                    all_panels.add(extra_panel)
-
-        # add OMIM to every panel choice
-        all_panels.add(GenePanelMasterList.OMIM_AUTO)
-        # add PANELAPP-GREEN to every panel choice
-        all_panels.add(GenePanelMasterList.PANELAPP_GREEN)
-
+        all_panels: set[str] = add_gene_panel_combo(default_panels=default_panels)
+        all_panels |= {GenePanelMasterList.OMIM_AUTO, GenePanelMasterList.PANELAPP_GREEN}
         return list(all_panels)
 
     def _get_latest_raw_file(self, family_id: str, tags: list[str]) -> Any: