Add nextflow workflow stub runs for tower runs (#3763) | major

### Added - Add nextflow workflow stub-run option for tower runs ### Changed - Removed log option for nextflow workflow start and run commands to keep option number under 13 ### Fixed -
Clinical-Genomics · Sep 25, 2024 · 97035c9 · 97035c9
1 parent 08878a5
commit 97035c9
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Showing 4 changed files with 22 additions and 20 deletions.
diff --git a/cg/cli/workflow/nf_analysis.py b/cg/cli/workflow/nf_analysis.py
@@ -37,12 +37,6 @@
     help="Choose a configuration profile",
 )
 
-OPTION_LOG = click.option(
-    "--log",
-    type=click.Path(),
-    help="Set nextflow log file path",
-)
-
 OPTION_CONFIG = click.option(
     "--config",
     type=click.Path(),
@@ -88,6 +82,13 @@
     show_default=True,
     help="Start workflow from start without resuming execution",
 )
+OPTION_STUB = click.option(
+    "--stub-run",
+    is_flag=True,
+    default=False,
+    show_default=True,
+    help="Start a stub workflow",
+)
 
 
 @click.command("config-case")
@@ -106,7 +107,6 @@ def config_case(context: CGConfig, case_id: str, dry_run: bool) -> None:
 
 @click.command("run")
 @ARGUMENT_CASE_ID
-@OPTION_LOG
 @OPTION_WORKDIR
 @OPTION_FROM_START
 @OPTION_PROFILE
@@ -116,12 +116,12 @@ def config_case(context: CGConfig, case_id: str, dry_run: bool) -> None:
 @OPTION_COMPUTE_ENV
 @OPTION_USE_NEXTFLOW
 @OPTION_TOWER_RUN_ID
+@OPTION_STUB
 @DRY_RUN
 @click.pass_obj
 def run(
     context: CGConfig,
     case_id: str,
-    log: str,
     work_dir: str,
     from_start: bool,
     profile: str,
@@ -131,6 +131,7 @@ def run(
     compute_env: str,
     use_nextflow: bool,
     nf_tower_id: str | None,
+    stub_run: bool,
     dry_run: bool,
 ) -> None:
     """Run analysis for a case."""
@@ -139,7 +140,6 @@ def run(
         analysis_api.run_nextflow_analysis(
             case_id=case_id,
             dry_run=dry_run,
-            log=log,
             work_dir=work_dir,
             from_start=from_start,
             profile=profile,
@@ -149,6 +149,7 @@ def run(
             compute_env=compute_env,
             use_nextflow=use_nextflow,
             nf_tower_id=nf_tower_id,
+            stub_run=stub_run,
         )
     except Exception as error:
         LOG.error(f"Unspecified error occurred: {error}")
@@ -157,27 +158,27 @@ def run(
 
 @click.command("start")
 @ARGUMENT_CASE_ID
-@OPTION_LOG
 @OPTION_WORKDIR
 @OPTION_PROFILE
 @OPTION_CONFIG
 @OPTION_PARAMS_FILE
 @OPTION_REVISION
 @OPTION_COMPUTE_ENV
 @OPTION_USE_NEXTFLOW
+@OPTION_STUB
 @DRY_RUN
 @click.pass_obj
 def start(
     context: CGConfig,
     case_id: str,
-    log: str,
     work_dir: str,
     profile: str,
     config: str,
     params_file: str,
     revision: str,
     compute_env: str,
     use_nextflow: bool,
+    stub_run: bool,
     dry_run: bool,
 ) -> None:
     """Start workflow for a case."""
@@ -190,7 +191,6 @@ def start(
         analysis_api.run_nextflow_analysis(
             case_id=case_id,
             dry_run=dry_run,
-            log=log,
             work_dir=work_dir,
             from_start=True,
             profile=profile,
@@ -199,6 +199,7 @@ def start(
             revision=revision,
             compute_env=compute_env,
             use_nextflow=use_nextflow,
+            stub_run=stub_run,
         )
     except Exception as error:
         LOG.error(f"Unexpected error occurred: {error}")

diff --git a/cg/meta/workflow/nf_analysis.py b/cg/meta/workflow/nf_analysis.py
@@ -207,10 +207,8 @@ def create_case_directory(self, case_id: str, dry_run: bool = False) -> None:
         if not dry_run:
             Path(self.get_case_path(case_id=case_id)).mkdir(parents=True, exist_ok=True)
 
-    def get_log_path(self, case_id: str, workflow: str, log: str = None) -> Path:
+    def get_log_path(self, case_id: str, workflow: str) -> Path:
         """Path to NF log."""
-        if log:
-            return log
         launch_time: str = datetime.now().strftime("%Y-%m-%d_%H.%M.%S")
         return Path(
             self.get_case_path(case_id),
@@ -453,7 +451,6 @@ def _run_analysis_with_tower(
     def get_command_args(
         self,
         case_id: str,
-        log: str,
         work_dir: str,
         from_start: bool,
         profile: str,
@@ -462,10 +459,11 @@ def get_command_args(
         revision: str,
         compute_env: str,
         nf_tower_id: str | None,
+        stub_run: bool,
     ) -> NfCommandArgs:
         command_args: NfCommandArgs = NfCommandArgs(
             **{
-                "log": self.get_log_path(case_id=case_id, workflow=self.workflow, log=log),
+                "log": self.get_log_path(case_id=case_id, workflow=self.workflow),
                 "work_dir": self.get_workdir_path(case_id=case_id, work_dir=work_dir),
                 "resume": not from_start,
                 "profile": self.get_profile(profile=profile),
@@ -476,6 +474,7 @@ def get_command_args(
                 "revision": revision or self.revision,
                 "wait": NfTowerStatus.SUBMITTED,
                 "id": nf_tower_id,
+                "stub_run": stub_run,
             }
         )
         return command_args
@@ -484,14 +483,14 @@ def run_nextflow_analysis(
         self,
         case_id: str,
         use_nextflow: bool,
-        log: str,
         work_dir: str,
         from_start: bool,
         profile: str,
         config: str,
         params_file: str | None,
         revision: str,
         compute_env: str,
+        stub_run: bool,
         nf_tower_id: str | None = None,
         dry_run: bool = False,
     ) -> None:
@@ -500,7 +499,6 @@ def run_nextflow_analysis(
 
         command_args = self.get_command_args(
             case_id=case_id,
-            log=log,
             work_dir=work_dir,
             from_start=from_start,
             profile=profile,
@@ -509,6 +507,7 @@ def run_nextflow_analysis(
             revision=revision,
             compute_env=compute_env,
             nf_tower_id=nf_tower_id,
+            stub_run=stub_run,
         )
 
         try:

diff --git a/cg/meta/workflow/nf_handlers.py b/cg/meta/workflow/nf_handlers.py
@@ -44,6 +44,7 @@ def get_tower_launch_parameters(cls, tower_workflow: str, command_args: dict) ->
                     "name",
                     "revision",
                     "compute_env",
+                    "stub_run",
                 )
             },
             exclude_true=True,
@@ -62,6 +63,7 @@ def get_tower_relaunch_parameters(cls, from_tower_id: int, command_args: dict) -
                     "params_file",
                     "config",
                     "compute_env",
+                    "stub_run",
                 )
             },
             exclude_true=True,

diff --git a/cg/models/nf_analysis.py b/cg/models/nf_analysis.py
@@ -16,7 +16,7 @@ class NfCommandArgs(BaseModel):
     log: str | Path | None
     resume: bool | None
     profile: str | None
-    stub: bool | None
+    stub_run: bool | None
     config: str | Path | None
     name: str | None
     revision: str | None