Add workflow Nallo start (#4112)

### Added - workflow nallo start
Clinical-Genomics · Jan 20, 2025 · f18df85 · f18df85
1 parent c954a4b
commit f18df85
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Showing 4 changed files with 9 additions and 4 deletions.
diff --git a/cg/cli/workflow/nallo/base.py b/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
+from cg.cli.workflow.nf_analysis import config_case, run, start
 
 from cg.constants.constants import MetaApis
 from cg.meta.workflow.analysis import AnalysisAPI
@@ -25,3 +25,4 @@ def nallo(context: click.Context) -> None:
 
 nallo.add_command(config_case)
 nallo.add_command(run)
+nallo.add_command(start)
diff --git a/cg/cli/workflow/nf_analysis.py b/cg/cli/workflow/nf_analysis.py
@@ -7,13 +7,14 @@
 
 from cg.cli.workflow.commands import ARGUMENT_CASE_ID
 from cg.cli.workflow.utils import validate_force_store_option
-from cg.constants import EXIT_FAIL, EXIT_SUCCESS
+from cg.constants import EXIT_FAIL, EXIT_SUCCESS, Workflow
 from cg.constants.cli_options import DRY_RUN, FORCE, COMMENT
 from cg.constants.constants import MetaApis
 from cg.exc import AnalysisNotReadyError, CgError, HousekeeperStoreError
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
 
 from cg.models.cg_config import CGConfig
+from cg.store.models import Case
 
 LOG = logging.getLogger(__name__)
 
@@ -186,7 +187,9 @@ def start(
     analysis_api: NfAnalysisAPI = context.meta_apis[MetaApis.ANALYSIS_API]
     try:
         analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
-        analysis_api.prepare_fastq_files(case_id=case_id, dry_run=dry_run)
+        case: Case = analysis_api.status_db.get_case_by_internal_id(case_id)
+        if case.data_analysis != Workflow.NALLO:
+            analysis_api.prepare_fastq_files(case_id=case_id, dry_run=dry_run)
         analysis_api.config_case(case_id=case_id, dry_run=dry_run)
         analysis_api.run_nextflow_analysis(
             case_id=case_id,

diff --git a/cg/services/sequencing_qc_service/quality_checks/checks.py b/cg/services/sequencing_qc_service/quality_checks/checks.py
@@ -33,6 +33,7 @@ def get_sequencing_quality_check_for_case(case: Case) -> Callable:
         Workflow.BALSAMIC_UMI,
         Workflow.MIP_DNA,
         Workflow.MIP_RNA,
+        Workflow.NALLO,
         Workflow.RAREDISEASE,
         Workflow.RNAFUSION,
         Workflow.TOMTE,

diff --git a/tests/cli/workflow/nf_analysis/test_cli_start.py b/tests/cli/workflow/nf_analysis/test_cli_start.py
@@ -16,7 +16,7 @@
 
 @pytest.mark.parametrize(
     "workflow",
-    NEXTFLOW_WORKFLOWS,
+    NEXTFLOW_WORKFLOWS + [Workflow.NALLO],
 )
 def test_start(
     cli_runner: CliRunner,