Add Nallo workflow metrics-deliver

cg/cli/workflow/nallo/base.py

@@ -6,7 +6,7 @@
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 
-from cg.cli.workflow.nf_analysis import config_case, run, start
+from cg.cli.workflow.nf_analysis import config_case, run, start, metrics_deliver
 
 from cg.constants.constants import MetaApis
 from cg.meta.workflow.analysis import AnalysisAPI
@@ -26,3 +26,4 @@ def nallo(context: click.Context) -> None:
 nallo.add_command(config_case)
 nallo.add_command(run)
 nallo.add_command(start)
+nallo.add_command(metrics_deliver)

cg/constants/nf_analysis.py

@@ -15,6 +15,10 @@ class NfTowerStatus(StrEnum):
     UNKNOWN: str = "UNKNOWN"
 
 
+NALLO_METRIC_CONDITIONS: dict[str, dict[str, Any]] = {
+    "median_coverage": {"norm": "gt", "threshold": 25},
+}
+
 RAREDISEASE_PREDICTED_SEX_METRIC = "predicted_sex_sex_check"
 
 RAREDISEASE_METRIC_CONDITIONS: dict[str, dict[str, Any]] = {

cg/meta/workflow/nallo.py

@@ -1,7 +1,9 @@
 """Module for Nallo Analysis API."""
 
 import logging
+
 from cg.constants import Workflow
+from cg.constants.nf_analysis import NALLO_METRIC_CONDITIONS
 from cg.constants.subject import PlinkPhenotypeStatus, PlinkSex
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
 from cg.models.cg_config import CGConfig
@@ -91,3 +93,6 @@ def get_built_workflow_parameters(self, case_id: str) -> NalloParameters:
             input=self.get_sample_sheet_path(case_id=case_id),
             outdir=outdir,
         )
+
+    def get_workflow_metrics(self, metric_id: str) -> dict:
+        return NALLO_METRIC_CONDITIONS

cg/models/nallo/nallo.py

@@ -7,6 +7,12 @@
 from cg.models.nf_analysis import WorkflowParameters
 
 
+class NalloQCMetrics(BaseModel):
+    """Nallo QC metrics"""
+
+    median_coverage: float | None
+
+
 class NalloSampleSheetEntry(BaseModel):
     """Nallo sample model is used when building the sample sheet."""
 

tests/cli/workflow/nf_analysis/test_cli_config_case.py

@@ -44,7 +44,7 @@ def test_config_case_without_options(
 
 @pytest.mark.parametrize(
     "workflow",
-    NEXTFLOW_WORKFLOWS,
+    NEXTFLOW_WORKFLOWS + [Workflow.NALLO],
 )
 def test_config_with_missing_case(
     cli_runner: CliRunner,
@@ -74,7 +74,7 @@ def test_config_with_missing_case(
 
 @pytest.mark.parametrize(
     "workflow",
-    NEXTFLOW_WORKFLOWS,
+    NEXTFLOW_WORKFLOWS + [Workflow.NALLO],
 )
 def test_config_case_without_samples(
     cli_runner: CliRunner,
@@ -185,7 +185,7 @@ def test_config_case_default_parameters(
 
 @pytest.mark.parametrize(
     "workflow",
-    NEXTFLOW_WORKFLOWS,
+    NEXTFLOW_WORKFLOWS + [Workflow.NALLO],
 )
 def test_config_case_dry_run(
     cli_runner: CliRunner,

tests/cli/workflow/nf_analysis/test_cli_metrics_deliver.py

@@ -18,7 +18,13 @@
 
 @pytest.mark.parametrize(
     "workflow",
-    [Workflow.RAREDISEASE, Workflow.RNAFUSION, Workflow.TAXPROFILER, Workflow.TOMTE],
+    [
+        Workflow.RAREDISEASE,
+        Workflow.RNAFUSION,
+        Workflow.TAXPROFILER,
+        Workflow.TOMTE,
+        Workflow.NALLO,
+    ],
 )
 def test_metrics_deliver_without_options(
     cli_runner: CliRunner, workflow: Workflow, request: FixtureRequest
@@ -38,7 +44,13 @@ def test_metrics_deliver_without_options(
 
 @pytest.mark.parametrize(
     "workflow",
-    [Workflow.RAREDISEASE, Workflow.RNAFUSION, Workflow.TAXPROFILER, Workflow.TOMTE],
+    [
+        Workflow.RAREDISEASE,
+        Workflow.RNAFUSION,
+        Workflow.TAXPROFILER,
+        Workflow.TOMTE,
+        Workflow.NALLO,
+    ],
 )
 def test_metrics_deliver_with_missing_case(
     cli_runner: CliRunner,
@@ -69,7 +81,13 @@ def test_metrics_deliver_with_missing_case(
 
 @pytest.mark.parametrize(
     "workflow",
-    [Workflow.RAREDISEASE, Workflow.RNAFUSION, Workflow.TAXPROFILER, Workflow.TOMTE],
+    [
+        Workflow.RAREDISEASE,
+        Workflow.RNAFUSION,
+        Workflow.TAXPROFILER,
+        Workflow.TOMTE,
+        Workflow.NALLO,
+    ],
 )
 def test_metrics_deliver_case(
     cli_runner: CliRunner,

tests/cli/workflow/test_cli_workflow.py

@@ -21,6 +21,7 @@ def test_no_options(cli_runner: CliRunner, base_context: CGConfig):
     assert "microsalt" in result.output
     assert "mip-dna" in result.output
     assert "mip-rna" in result.output
+    assert "nallo" in result.output
     assert "raredisease" in result.output
     assert "rnafusion" in result.output
     assert "taxprofiler" in result.output

tests/conftest.py

@@ -868,6 +868,12 @@ def mip_dna_analysis_dir(mip_analysis_dir: Path) -> Path:
     return Path(mip_analysis_dir, "dna")
 
 
+@pytest.fixture
+def nallo_analysis_dir(analysis_dir: Path) -> Path:
+    """Return the path to the directory with nallo analysis files."""
+    return Path(analysis_dir, "nallo")
+
+
 @pytest.fixture
 def nf_analysis_analysis_dir(fixtures_dir: Path) -> Path:
     """Return the path to the directory with nf-analysis files."""
@@ -2115,7 +2121,7 @@ def context_config(
             "workflow_bin_path": Path("workflow", "path").as_posix(),
             "profile": "myprofile",
             "references": Path("path", "to", "references").as_posix(),
-            "revision": "dev",
+            "revision": "2.2.0",
             "root": str(nallo_dir),
             "slurm": {
                 "account": "development",
@@ -2523,7 +2529,7 @@ def bam_unmapped_read_paths(housekeeper_dir: Path) -> Path:
     """Path to existing bam read file."""
     bam_unmapped_read_path = Path(
         housekeeper_dir, "m00000_000000_000000_s4.hifi_reads.bc2021"
-    ).with_suffix(f"{AlignmentFileTag.BAM}")
+    ).with_suffix(f".{AlignmentFileTag.BAM}")
     with open(bam_unmapped_read_path, "wb") as wh:
         wh.write(
             b"1f 8b 08 04 00 00 00 00 00 ff 06 00 42 43 02 00 1b 00 03 00 00 00 00 00 00 00 00 00"
@@ -2541,7 +2547,7 @@ def sequencing_platform() -> str:
 @pytest.fixture(scope="session")
 def nallo_case_id() -> str:
     """Returns a nallo case id."""
-    return "nallo_case_two_samples"
+    return "nallo_case_enough_reads"
 
 
 @pytest.fixture(scope="function")
@@ -2550,62 +2556,88 @@ def nallo_context(
     helpers: StoreHelpers,
     nf_analysis_housekeeper: HousekeeperAPI,
     trailblazer_api: MockTB,
-    hermes_api: HermesApi,
-    cg_dir: Path,
     nallo_case_id: str,
     sample_id: str,
+    father_sample_id: str,
     sample_name: str,
     another_sample_name: str,
-    father_sample_id: str,
     no_sample_case_id: str,
+    total_sequenced_reads_pass: int,
     wgs_long_read_application_tag: str,
+    case_id_not_enough_reads: str,
+    sample_id_not_enough_reads: str,
+    total_sequenced_reads_not_pass: int,
 ) -> CGConfig:
-    """Context to use in CLI."""
+    """context to use in cli"""
     cg_context.housekeeper_api_ = nf_analysis_housekeeper
     cg_context.trailblazer_api_ = trailblazer_api
     cg_context.meta_apis["analysis_api"] = NalloAnalysisAPI(config=cg_context)
     status_db: Store = cg_context.status_db
 
+    # NB: the order in which the cases are added matters for the tests of store_available
+
     # Create ERROR case with NO SAMPLES
     helpers.add_case(status_db, internal_id=no_sample_case_id, name=no_sample_case_id)
 
-    # Create textbook case with two samples
-    nallo_case_two_samples: Case = helpers.add_case(
+    # Create textbook case with enough reads
+    case_enough_reads: Case = helpers.add_case(
         store=status_db,
         internal_id=nallo_case_id,
         name=nallo_case_id,
         data_analysis=Workflow.NALLO,
     )
 
-    nallo_sample_one: Sample = helpers.add_sample(
+    sample_enough_reads: Sample = helpers.add_sample(
         status_db,
         internal_id=sample_id,
         name=sample_name,
         last_sequenced_at=datetime.now(),
+        reads=total_sequenced_reads_pass,
         application_tag=wgs_long_read_application_tag,
         reference_genome=GenomeVersion.HG38,
     )
 
-    another_nallo_sample: Sample = helpers.add_sample(
+    another_sample_enough_reads: Sample = helpers.add_sample(
         status_db,
         internal_id=father_sample_id,
         name=another_sample_name,
         last_sequenced_at=datetime.now(),
+        reads=total_sequenced_reads_pass,
         application_tag=wgs_long_read_application_tag,
         reference_genome=GenomeVersion.HG38,
     )
 
     helpers.add_relationship(
         status_db,
-        case=nallo_case_two_samples,
-        sample=nallo_sample_one,
+        case=case_enough_reads,
+        sample=sample_enough_reads,
     )
 
     helpers.add_relationship(
         status_db,
-        case=nallo_case_two_samples,
-        sample=another_nallo_sample,
+        case=case_enough_reads,
+        sample=another_sample_enough_reads,
     )
+
+    # Create case without enough reads
+    case_not_enough_reads: Case = helpers.add_case(
+        store=status_db,
+        internal_id=case_id_not_enough_reads,
+        name=case_id_not_enough_reads,
+        data_analysis=Workflow.NALLO,
+    )
+
+    sample_not_enough_reads: Sample = helpers.add_sample(
+        status_db,
+        internal_id=sample_id_not_enough_reads,
+        last_sequenced_at=datetime.now(),
+        reads=total_sequenced_reads_not_pass,
+        application_tag=wgs_long_read_application_tag,
+        reference_genome=GenomeVersion.HG38,
+    )
+
+    helpers.add_relationship(status_db, case=case_not_enough_reads, sample=sample_not_enough_reads)
+
     return cg_context
 
 
@@ -2625,6 +2657,112 @@ def nallo_config(nallo_dir: Path, nallo_case_id: str) -> None:
     ).touch(exist_ok=True)
 
 
+@pytest.fixture(scope="function")
+def nallo_deliverable_data(nallo_dir: Path, nallo_case_id: str, sample_id: str) -> dict:
+    return {
+        "files": [
+            {
+                "path": f"{nallo_dir}/{nallo_case_id}/multiqc/multiqc_report.html",
+                "path_index": "",
+                "step": "report",
+                "tag": ["multiqc-html"],
+                "id": nallo_case_id,
+                "format": "html",
+                "mandatory": True,
+            },
+        ]
+    }
+
+
+@pytest.fixture(scope="function")
+def nallo_metrics_deliverables(nallo_analysis_dir: Path) -> list[dict]:
+    """Returns the content of a mock metrics deliverables file."""
+    return read_yaml(
+        file_path=Path(nallo_analysis_dir, "nallo_fixture_for_metrics_deliverables.yaml")
+    )
+
+
+@pytest.fixture(scope="function")
+def nallo_metrics_deliverables_path(nallo_dir: Path, nallo_case_id: str) -> Path:
+    """Path to deliverables file."""
+    return Path(nallo_dir, nallo_case_id, f"{nallo_case_id}_metrics_deliverables").with_suffix(
+        FileExtensions.YAML
+    )
+
+
+@pytest.fixture(scope="function")
+def nallo_mock_analysis_finish(
+    nallo_dir: Path,
+    nallo_case_id: str,
+    nallo_multiqc_json_metrics: dict,
+    tower_id: int,
+) -> None:
+    """Create analysis finish file for testing."""
+    Path.mkdir(Path(nallo_dir, nallo_case_id, "pipeline_info"), parents=True, exist_ok=True)
+    Path(nallo_dir, nallo_case_id, "pipeline_info", software_version_file).touch(exist_ok=True)
+    Path(nallo_dir, nallo_case_id, f"{nallo_case_id}_samplesheet.csv").touch(exist_ok=True)
+    Path.mkdir(
+        Path(nallo_dir, nallo_case_id, "multiqc", "multiqc_data"),
+        parents=True,
+        exist_ok=True,
+    )
+    write_json(
+        content=nallo_multiqc_json_metrics,
+        file_path=Path(
+            nallo_dir,
+            nallo_case_id,
+            "multiqc",
+            "multiqc_data",
+            "multiqc_data",
+        ).with_suffix(FileExtensions.JSON),
+    )
+    write_yaml(
+        content={nallo_case_id: [tower_id]},
+        file_path=Path(
+            nallo_dir,
+            nallo_case_id,
+            "tower_ids",
+        ).with_suffix(FileExtensions.YAML),
+    )
+
+
+@pytest.fixture(scope="function")
+def nallo_mock_deliverable_dir(
+    nallo_dir: Path, nallo_deliverable_data: dict, nallo_case_id: str
+) -> Path:
+    """Create nallo deliverable file with dummy data and files to deliver."""
+    Path.mkdir(
+        Path(nallo_dir, nallo_case_id),
+        parents=True,
+        exist_ok=True,
+    )
+    Path.mkdir(
+        Path(nallo_dir, nallo_case_id, "multiqc"),
+        parents=True,
+        exist_ok=True,
+    )
+    for report_entry in nallo_deliverable_data["files"]:
+        Path(report_entry["path"]).touch(exist_ok=True)
+    WriteFile.write_file_from_content(
+        content=nallo_deliverable_data,
+        file_format=FileFormat.JSON,
+        file_path=Path(nallo_dir, nallo_case_id, nallo_case_id + deliverables_yaml),
+    )
+    return nallo_dir
+
+
+@pytest.fixture
+def nallo_multiqc_json_metrics_path(nallo_analysis_dir: Path) -> Path:
+    """Return Multiqc JSON file path for nallo."""
+    return Path(nallo_analysis_dir, multiqc_json_file)
+
+
+@pytest.fixture(scope="function")
+def nallo_multiqc_json_metrics(nallo_analysis_dir) -> dict:
+    """Returns the content of a mock Multiqc JSON file."""
+    return read_json(file_path=Path(nallo_analysis_dir, multiqc_json_file))
+
+
 @pytest.fixture(scope="function")
 def nallo_nexflow_config_file_path(nallo_dir, nallo_case_id) -> Path:
     """Path to config file."""