Merge branch 'master' into feat-remove-bcl2fastq

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 54.4.6
+current_version = 54.4.8
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "54.4.6"
+__version__ = "54.4.8"

cg/constants/housekeeper_tags.py

@@ -194,4 +194,17 @@ class BalsamicProtectedTags:
         ["gisaid-log"],
         ["gisaid-csv"],
     ],
+    str(Pipeline.RNAFUSION): [
+        [AnalysisTag.FUSION, AnalysisTag.ARRIBA],
+        [AnalysisTag.FUSION, AnalysisTag.STARFUSION],
+        [AnalysisTag.FUSION, AnalysisTag.FUSIONCATCHER],
+        [AnalysisTag.FUSIONINSPECTOR],
+        [AnalysisTag.FUSIONREPORT, AnalysisTag.RESEARCH],
+        [AnalysisTag.FUSIONINSPECTOR_HTML, AnalysisTag.RESEARCH],
+        [AnalysisTag.ARRIBA_VISUALIZATION, AnalysisTag.RESEARCH],
+        [AnalysisTag.MULTIQC_HTML, AnalysisTag.RNA],
+        [HK_DELIVERY_REPORT_TAG],
+        [AnalysisTag.VCF_FUSION],
+        [AnalysisTag.GENE_COUNTS],
+    ],
 }

cg/meta/workflow/nf_analysis.py

@@ -205,6 +205,66 @@ def write_trailblazer_config(self, case_id: str, tower_id: str) -> None:
             file_path=config_path,
         )
 
+    def _run_analysis_with_nextflow(
+        self, case_id: str, command_args: CommandArgs, dry_run: bool
+    ) -> None:
+        """Run analysis with given options using Nextflow."""
+        self.process = Process(
+            binary=self.nextflow_binary_path,
+            environment=self.conda_env,
+            conda_binary=self.conda_binary,
+            launch_directory=self.get_case_path(case_id=case_id),
+        )
+        LOG.info("Pipeline will be executed using Nextflow")
+        parameters: list[str] = NextflowHandler.get_nextflow_run_parameters(
+            case_id=case_id,
+            pipeline_path=self.nfcore_pipeline_path,
+            root_dir=self.root_dir,
+            command_args=command_args.dict(),
+        )
+        self.process.export_variables(
+            export=NextflowHandler.get_variables_to_export(),
+        )
+        command: str = self.process.get_command(parameters=parameters)
+        LOG.info(f"{command}")
+        sbatch_number: int = NextflowHandler.execute_head_job(
+            case_id=case_id,
+            case_directory=self.get_case_path(case_id=case_id),
+            slurm_account=self.account,
+            email=self.email,
+            qos=self.get_slurm_qos_for_case(case_id=case_id),
+            commands=command,
+            dry_run=dry_run,
+        )
+        LOG.info(f"Nextflow head job running as job: {sbatch_number}")
+
+    def _run_analysis_with_tower(
+        self, case_id: str, command_args: CommandArgs, dry_run: bool
+    ) -> None:
+        """Run analysis with given options using NF-Tower."""
+        LOG.info("Pipeline will be executed using Tower")
+        if command_args.resume:
+            from_tower_id: int = command_args.id or NfTowerHandler.get_last_tower_id(
+                case_id=case_id,
+                trailblazer_config=self.get_trailblazer_config_path(case_id=case_id),
+            )
+            LOG.info(f"Pipeline will be resumed from run with Tower id: {from_tower_id}.")
+            parameters: list[str] = NfTowerHandler.get_tower_relaunch_parameters(
+                from_tower_id=from_tower_id, command_args=command_args.dict()
+            )
+        else:
+            parameters: list[str] = NfTowerHandler.get_tower_launch_parameters(
+                tower_pipeline=self.tower_pipeline,
+                command_args=command_args.dict(),
+            )
+        self.process.run_command(parameters=parameters, dry_run=dry_run)
+        if self.process.stderr:
+            LOG.error(self.process.stderr)
+        if not dry_run:
+            tower_id = NfTowerHandler.get_tower_id(stdout_lines=self.process.stdout_lines())
+            self.write_trailblazer_config(case_id=case_id, tower_id=tower_id)
+        LOG.info(self.process.stdout)
+
     def run_analysis(
         self,
         case_id: str,
@@ -214,61 +274,17 @@ def run_analysis(
     ) -> None:
         """Execute run analysis with given options."""
         if use_nextflow:
-            self.process = Process(
-                binary=self.nextflow_binary_path,
-                environment=self.conda_env,
-                conda_binary=self.conda_binary,
-                launch_directory=self.get_case_path(case_id=case_id),
-            )
-            LOG.info("Pipeline will be executed using nextflow")
-            parameters: list[str] = NextflowHandler.get_nextflow_run_parameters(
+            self._run_analysis_with_nextflow(
                 case_id=case_id,
-                pipeline_path=self.nfcore_pipeline_path,
-                root_dir=self.root_dir,
-                command_args=command_args.dict(),
-            )
-            self.process.export_variables(
-                export=NextflowHandler.get_variables_to_export(),
+                command_args=command_args,
+                dry_run=dry_run,
             )
-
-            command = self.process.get_command(parameters=parameters)
-            LOG.info(f"{command}")
-            sbatch_number: int = NextflowHandler.execute_head_job(
+        else:
+            self._run_analysis_with_tower(
                 case_id=case_id,
-                case_directory=self.get_case_path(case_id=case_id),
-                slurm_account=self.account,
-                email=self.email,
-                qos=self.get_slurm_qos_for_case(case_id=case_id),
-                commands=command,
+                command_args=command_args,
                 dry_run=dry_run,
             )
-            LOG.info(f"Nextflow head job running as job {sbatch_number}")
-
-        else:
-            LOG.info("Pipeline will be executed using tower")
-            if command_args.resume:
-                from_tower_id: int = command_args.id
-                if not from_tower_id:
-                    from_tower_id: int = NfTowerHandler.get_last_tower_id(
-                        case_id=case_id,
-                        trailblazer_config=self.get_trailblazer_config_path(case_id=case_id),
-                    )
-                LOG.info(f"Pipeline will be resumed from run {from_tower_id}.")
-                parameters: list[str] = NfTowerHandler.get_tower_relaunch_parameters(
-                    from_tower_id=from_tower_id, command_args=command_args.dict()
-                )
-            else:
-                parameters: list[str] = NfTowerHandler.get_tower_launch_parameters(
-                    tower_pipeline=self.tower_pipeline,
-                    command_args=command_args.dict(),
-                )
-            self.process.run_command(parameters=parameters, dry_run=dry_run)
-            if self.process.stderr:
-                LOG.error(self.process.stderr)
-            if not dry_run:
-                tower_id = NfTowerHandler.get_tower_id(stdout_lines=self.process.stdout_lines())
-                self.write_trailblazer_config(case_id=case_id, tower_id=tower_id)
-            LOG.info(self.process.stdout)
 
     @staticmethod
     def get_deliverables_template_content() -> list[dict]:

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "54.4.6"
+version = "54.4.8"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"

tests/cli/workflow/rnafusion/test_cli_rnafusion_run.py

@@ -116,7 +116,7 @@ def test_with_config_use_nextflow(
     assert result.exit_code == EXIT_SUCCESS
 
     # THEN command should use nextflow
-    assert "using nextflow" in caplog.text
+    assert "using Nextflow" in caplog.text
     assert "path/to/bin/nextflow" in caplog.text
     assert "-work-dir" in caplog.text
 
@@ -145,7 +145,7 @@ def test_with_config(
     assert result.exit_code == EXIT_SUCCESS
 
     # THEN command should use tower
-    assert "using tower" in caplog.text
+    assert "using Tower" in caplog.text
     assert "path/to/bin/tw launch" in caplog.text
     assert "--work-dir" in caplog.text
 

tests/cli/workflow/taxprofiler/test_cli_taxprofiler_run.py

@@ -65,7 +65,7 @@ def test_with_config_use_nextflow(
     assert result.exit_code == EXIT_SUCCESS
 
     for message in [
-        "using nextflow",
+        "using Nextflow",
         "path/to/bin/nextflow",
         "-work-dir",
         "-params-file",
@@ -97,7 +97,7 @@ def test_with_config_use_tower(
     # THEN command should use tower
 
     for message in [
-        "using tower",
+        "using Tower",
         "path/to/bin/tw launch",
     ]:
         assert message in caplog.text