(feat taxprofiler): Add report-deliver (#2912)(minor)

### Added

- cg workflow taxprofiler report-deliver case_id

cg/cli/workflow/nf_analysis.py

@@ -1,13 +1,18 @@
 """CLI options for Nextflow and NF-Tower."""
 
+import logging
+
 import click
+from pydantic.v1 import ValidationError
 
 from cg.cli.workflow.commands import ARGUMENT_CASE_ID, OPTION_DRY
 from cg.constants.constants import MetaApis
 from cg.exc import CgError
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
 from cg.models.cg_config import CGConfig
 
+LOG = logging.getLogger(__name__)
+
 OPTION_WORKDIR = click.option(
     "--work-dir",
     type=click.Path(),
@@ -91,3 +96,24 @@ def metrics_deliver(context: CGConfig, case_id: str, dry_run: bool) -> None:
         analysis_api.validate_qc_metrics(case_id=case_id, dry_run=dry_run)
     except CgError as error:
         raise click.Abort() from error
+
+
+@click.command("report-deliver")
+@ARGUMENT_CASE_ID
+@OPTION_DRY
+@click.pass_obj
+def report_deliver(context: CGConfig, case_id: str, dry_run: bool) -> None:
+    """Create a Housekeeper deliverables file for given case id."""
+
+    analysis_api: NfAnalysisAPI = context.meta_apis[MetaApis.ANALYSIS_API]
+
+    try:
+        analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
+        analysis_api.trailblazer_api.is_latest_analysis_completed(case_id=case_id)
+        if not dry_run:
+            analysis_api.report_deliver(case_id=case_id)
+        else:
+            LOG.info(f"Dry-run: Would have created delivery files for case {case_id}")
+    except Exception as error:
+        LOG.error(f"Could not create report file: {error}")
+        raise click.Abort()

cg/cli/workflow/rnafusion/base.py

@@ -19,6 +19,7 @@
     OPTION_USE_NEXTFLOW,
     OPTION_WORKDIR,
     metrics_deliver,
+    report_deliver,
 )
 from cg.cli.workflow.rnafusion.options import (
     OPTION_FROM_START,
@@ -222,30 +223,7 @@ def start_available(context: click.Context, dry_run: bool = False) -> None:
 
 
 rnafusion.add_command(metrics_deliver)
-
-
-@rnafusion.command("report-deliver")
-@ARGUMENT_CASE_ID
-@DRY_RUN
-@click.pass_obj
-def report_deliver(context: CGConfig, case_id: str, dry_run: bool) -> None:
-    """Create a housekeeper deliverables file for given CASE ID."""
-
-    analysis_api: RnafusionAnalysisAPI = context.meta_apis[MetaApis.ANALYSIS_API]
-
-    try:
-        analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
-        analysis_api.trailblazer_api.is_latest_analysis_completed(case_id=case_id)
-        if not dry_run:
-            analysis_api.report_deliver(case_id=case_id)
-        else:
-            LOG.info("Dry-run")
-    except (CgError, ValidationError) as error:
-        LOG.error(f"Could not create report file: {error}")
-        raise click.Abort()
-    except Exception as error:
-        LOG.error(f"Could not create report file: {error}")
-        raise click.Abort()
+rnafusion.add_command(report_deliver)
 
 
 @rnafusion.command("store-housekeeper")

cg/cli/workflow/taxprofiler/base.py

@@ -17,6 +17,7 @@
     OPTION_USE_NEXTFLOW,
     OPTION_WORKDIR,
     metrics_deliver,
+    report_deliver,
 )
 from cg.cli.workflow.taxprofiler.options import OPTION_FROM_START, OPTION_INSTRUMENT_PLATFORM
 from cg.constants import EXIT_FAIL, EXIT_SUCCESS
@@ -42,6 +43,7 @@ def taxprofiler(context: click.Context) -> None:
 
 taxprofiler.add_command(resolve_compression)
 taxprofiler.add_command(metrics_deliver)
+taxprofiler.add_command(report_deliver)
 
 
 @taxprofiler.command("config-case")

cg/meta/workflow/nf_analysis.py

@@ -19,9 +19,10 @@
     MetricsDeliverablesCondition,
 )
 from cg.models.fastq import FastqFileMeta
-from cg.models.nf_analysis import FileDeliverable, PipelineDeliverables
+from cg.models.nf_analysis import FileDeliverable, WorkflowDeliverables
 from cg.models.rnafusion.rnafusion import CommandArgs
 from cg.utils import Process
+from cg.store.models import Sample
 
 LOG = logging.getLogger(__name__)
 
@@ -307,27 +308,69 @@ def run_analysis(
                 dry_run=dry_run,
             )
 
-    @staticmethod
-    def get_deliverables_template_content() -> list[dict]:
+    def get_deliverables_template_content(self) -> list[dict]:
         """Return deliverables file template content."""
         raise NotImplementedError
 
-    def get_deliverables_for_case(self, case_id: str) -> PipelineDeliverables:
-        """Return PipelineDeliverables for a given case."""
-        deliverable_template: list[dict] = self.get_deliverables_template_content()
-        sample_id: str = self.status_db.get_samples_by_case_id(case_id).pop().internal_id
+    def get_bundle_filenames_path(self) -> Path | None:
+        """Return bundle filenames path."""
+        return None
+
+    @staticmethod
+    def get_formatted_file_deliverable(
+        file_template: dict[str | None, str | None],
+        case_id: str,
+        sample_id: str,
+        sample_name: str,
+        case_path: str,
+    ) -> FileDeliverable:
+        """Return the formatted file deliverable with the case and sample attributes."""
+        deliverables = file_template.copy()
+        for deliverable_field, deliverable_value in file_template.items():
+            if deliverable_value is None:
+                continue
+            deliverables[deliverable_field] = (
+                deliverables[deliverable_field]
+                .replace("CASEID", case_id)
+                .replace("SAMPLEID", sample_id)
+                .replace("SAMPLENAME", sample_name)
+                .replace("PATHTOCASE", case_path)
+            )
+        return FileDeliverable(**deliverables)
+
+    def get_deliverables_for_sample(
+        self, sample: Sample, case_id: str, template: list[dict[str, str]]
+    ) -> list[FileDeliverable]:
+        """Return a list of FileDeliverables for each sample."""
+        sample_id: str = sample.internal_id
+        sample_name: str = sample.name
+        case_path = str(self.get_case_path(case_id=case_id))
         files: list[FileDeliverable] = []
-        for file in deliverable_template:
-            for deliverable_field, deliverable_value in file.items():
-                if deliverable_value is None:
-                    continue
-                file[deliverable_field] = file[deliverable_field].replace("CASEID", case_id)
-                file[deliverable_field] = file[deliverable_field].replace("SAMPLEID", sample_id)
-                file[deliverable_field] = file[deliverable_field].replace(
-                    "PATHTOCASE", str(self.get_case_path(case_id=case_id))
+        for file in template:
+            files.append(
+                self.get_formatted_file_deliverable(
+                    file_template=file,
+                    case_id=case_id,
+                    sample_id=sample_id,
+                    sample_name=sample_name,
+                    case_path=case_path,
                 )
-            files.append(FileDeliverable(**file))
-        return PipelineDeliverables(files=files)
+            )
+        return files
+
+    def get_deliverables_for_case(self, case_id: str) -> WorkflowDeliverables:
+        """Return workflow deliverables for a given case."""
+        deliverable_template: list[dict] = self.get_deliverables_template_content()
+        samples: list[Sample] = self.status_db.get_samples_by_case_id(case_id=case_id)
+        files: list[FileDeliverable] = []
+
+        for sample in samples:
+            bundles_per_sample = self.get_deliverables_for_sample(
+                sample=sample, case_id=case_id, template=deliverable_template
+            )
+            files.extend(bundle for bundle in bundles_per_sample if bundle not in files)
+
+        return WorkflowDeliverables(files=files)
 
     def get_multiqc_json_path(self, case_id: str) -> Path:
         """Return the path of the multiqc_data.json file."""
@@ -415,3 +458,14 @@ def validate_qc_metrics(self, case_id: str, dry_run: bool = False) -> None:
             self.trailblazer_api.set_analysis_status(case_id=case_id, status=AnalysisStatus.ERROR)
             raise CgError from error
         self.trailblazer_api.set_analysis_status(case_id=case_id, status=AnalysisStatus.COMPLETED)
+
+    def report_deliver(self, case_id: str) -> None:
+        """Write deliverables file."""
+        workflow_content: WorkflowDeliverables = self.get_deliverables_for_case(case_id=case_id)
+        self.write_deliverables_file(
+            deliverables_content=workflow_content.dict(),
+            file_path=self.get_deliverables_file_path(case_id=case_id),
+        )
+        LOG.info(
+            f"Writing deliverables file in {self.get_deliverables_file_path(case_id=case_id).as_posix()}"
+        )

cg/meta/workflow/rnafusion.py

@@ -8,14 +8,14 @@
 from cg.constants import Workflow
 from cg.constants.constants import FileFormat, Strandedness
 from cg.constants.nf_analysis import MULTIQC_NEXFLOW_CONFIG, RNAFUSION_METRIC_CONDITIONS
+from cg.resources import RNAFUSION_BUNDLE_FILENAMES_PATH
 from cg.exc import MissingMetrics
 from cg.io.controller import ReadFile
 from cg.io.json import read_json
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
 from cg.models.cg_config import CGConfig
 from cg.models.deliverables.metric_deliverables import MetricsBase, MultiqcDataJson
 from cg.models.fastq import FastqFileMeta
-from cg.models.nf_analysis import PipelineDeliverables
 from cg.models.rnafusion.rnafusion import (
     RnafusionAnalysis,
     RnafusionParameters,
@@ -56,18 +56,22 @@ def use_read_count_threshold(self) -> bool:
         when determining if the analysis for a case should be automatically started."""
         return True
 
-    @staticmethod
-    def get_deliverables_template_content() -> list[dict]:
+    def get_deliverables_template_content(self) -> list[dict]:
         """Return deliverables file template content."""
         return ReadFile.get_content_from_file(
             file_format=FileFormat.YAML,
-            file_path=resources.RNAFUSION_BUNDLE_FILENAMES_PATH,
+            file_path=self.get_bundle_filenames_path(),
         )
 
     def get_nextflow_config_content(self) -> str:
         """Return nextflow config content."""
         return MULTIQC_NEXFLOW_CONFIG
 
+    @staticmethod
+    def get_bundle_filenames_path() -> Path:
+        """Return Rnafusion bundle filenames path."""
+        return RNAFUSION_BUNDLE_FILENAMES_PATH
+
     def get_sample_sheet_content_per_sample(
         self, sample: Sample, case_id: str, strandedness: Strandedness
     ) -> list[list[str]]:
@@ -168,17 +172,6 @@ def get_multiqc_json_metrics(self, case_id: str) -> list[MetricsBase]:
         )
         return metric_base_list
 
-    def report_deliver(self, case_id: str) -> None:
-        """Create deliverables file."""
-        deliverables_content: PipelineDeliverables = self.get_deliverables_for_case(case_id=case_id)
-        self.write_deliverables_file(
-            deliverables_content=deliverables_content.dict(),
-            file_path=self.get_deliverables_file_path(case_id=case_id),
-        )
-        LOG.info(
-            f"Writing deliverables file in {self.get_deliverables_file_path(case_id=case_id).as_posix()}"
-        )
-
     @staticmethod
     def ensure_mandatory_metrics_present(metrics: list[MetricsBase]) -> None:
         """Check that all mandatory metrics are present. Raise error if missing."""

cg/meta/workflow/taxprofiler.py

@@ -6,12 +6,15 @@
 
 from cg.constants import Workflow
 from cg.constants.nf_analysis import MULTIQC_NEXFLOW_CONFIG
-from cg.constants.sequencing import SequencingPlatform
 from cg.io.json import read_json
+from cg.resources import TAXPROFILER_BUNDLE_FILENAMES_PATH
+from cg.constants.sequencing import SequencingPlatform
+from cg.constants.constants import FileFormat
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
 from cg.models.cg_config import CGConfig
 from cg.models.deliverables.metric_deliverables import MetricsBase, MultiqcDataJson
 from cg.models.fastq import FastqFileMeta
+from cg.io.controller import ReadFile
 from cg.models.taxprofiler.taxprofiler import (
     TaxprofilerParameters,
     TaxprofilerSampleSheetEntry,
@@ -50,6 +53,10 @@ def get_nextflow_config_content(self) -> str:
         """Return nextflow config content."""
         return MULTIQC_NEXFLOW_CONFIG
 
+    def get_bundle_filenames_path(self) -> Path:
+        """Return Taxprofiler bundle filenames path."""
+        return TAXPROFILER_BUNDLE_FILENAMES_PATH
+
     def get_sample_sheet_content_per_sample(
         self, sample: Sample, instrument_platform: SequencingPlatform.ILLUMINA, fasta: str = ""
     ) -> list[list[str]]:
@@ -158,3 +165,10 @@ def parse_multiqc_json_for_sample(sample_name: str, multiqc_json: list[dict]) ->
                     metrics_values.update(sample_values)
 
         return metrics_values
+
+    def get_deliverables_template_content(self) -> list[dict[str, str]]:
+        """Return deliverables file template content."""
+        return ReadFile.get_content_from_file(
+            file_format=FileFormat.YAML,
+            file_path=self.get_bundle_filenames_path(),
+        )

cg/models/nf_analysis.py

@@ -58,7 +58,7 @@ def set_path_as_string(cls, file_path: str | Path) -> str | None:
         return None
 
 
-class PipelineDeliverables(BaseModel):
+class WorkflowDeliverables(BaseModel):
     """Specification for workflow deliverables."""
 
     files: list[FileDeliverable]

cg/models/taxprofiler/taxprofiler.py

@@ -34,6 +34,9 @@ class TaxprofilerParameters(PipelineParameters):
     run_kraken2: bool = True
     kraken2_save_reads: bool = True
     kraken2_save_readclassification: bool = True
+    run_bracken: bool = True
+    run_centrifuge: bool = True
+    centrifuge_save_reads: bool = True
     run_krona: bool = True
     run_profile_standardisation: bool = True
 

cg/resources/__init__.py

@@ -8,6 +8,12 @@
 
 RNAFUSION_BUNDLE_FILENAMES: str = Path("resources", "rnafusion_bundle_filenames.csv").as_posix()
 
+TAXPROFILER_BUNDLE_FILENAMES: str = Path("resources", "taxprofiler_bundle_filenames.csv").as_posix()
+
 RNAFUSION_BUNDLE_FILENAMES_PATH: Path = Path(
     pkg_resources.resource_filename("cg", RNAFUSION_BUNDLE_FILENAMES)
 )
+
+TAXPROFILER_BUNDLE_FILENAMES_PATH: Path = Path(
+    pkg_resources.resource_filename("cg", TAXPROFILER_BUNDLE_FILENAMES)
+)