conflcit

latch/types/metadata.py

@@ -537,4 +537,18 @@ def __post_init__(self):
         _snakemake_metadata = self
 
 
+@dataclass
+class NextflowMetadata(LatchMetadata):
+    name: Optional[str] = None
+    parameters: Dict[str, SnakemakeParameter] = field(default_factory=dict)
+
+    def __post_init__(self):
+        if self.name is None:
+            self.name = f"nf_{identifier_suffix_from_str(self.display_name.lower())}"
+
+        global _nextflow_metadata
+        _nextflow_metadata = self
+
+
 _snakemake_metadata: Optional[SnakemakeMetadata] = None
+_nextflow_metadata: Optional[NextflowMetadata] = None

latch_cli/centromere/ctx.py

@@ -61,6 +61,7 @@ class _CentromereCtx:
     default_container: _Container
     workflow_type: WorkflowType
     snakefile: Optional[Path]
+    nf_script: Optional[Path]
 
     latch_register_api_url = config.api.workflow.register
     latch_image_api_url = config.api.workflow.upload_image
@@ -82,6 +83,7 @@ def __init__(
         disable_auto_version: bool = False,
         remote: bool = False,
         snakefile: Optional[Path] = None,
+        nf_script: Optional[Path] = None,
         use_new_centromere: bool = False,
     ):
         self.use_new_centromere = use_new_centromere
@@ -95,11 +97,20 @@ def __init__(
             self.dkr_repo = config.dkr_repo
             self.pkg_root = pkg_root.resolve()
 
-            if snakefile is None:
-                self.workflow_type = WorkflowType.latchbiosdk
-            else:
+            if snakefile and nf_script:
+                raise ValueError(
+                    "Cannot provide both a snakefile and nextflow script to the"
+                    " register command."
+                )
+
+            if snakefile is not None:
                 self.workflow_type = WorkflowType.snakemake
                 self.snakefile = snakefile
+            elif nf_script is not None:
+                self.workflow_type = WorkflowType.nextflow
+                self.nf_script = nf_script
+            else:
+                self.workflow_type = WorkflowType.latchbiosdk
 
             self.container_map: Dict[str, _Container] = {}
             if self.workflow_type == WorkflowType.latchbiosdk:
@@ -128,7 +139,7 @@ def __init__(
                         fg="red",
                     )
                     raise click.exceptions.Exit(1)
-            else:
+            elif self.workflow_type == WorkflowType.snakemake:
                 assert snakefile is not None
 
                 import latch.types.metadata as metadata
@@ -166,11 +177,13 @@ def __init__(
                             fg="red",
                         )
                         click.secho(
-                            "\nIt is possible to avoid including the Snakefile"
-                            " prior to registration by providing a"
-                            " `latch_metadata.py` file in the workflow root.\nThis"
-                            " way it is not necessary to install dependencies or"
-                            " ensure that Snakemake inputs locally.",
+                            (
+                                "\nIt is possible to avoid including the Snakefile"
+                                " prior to registration by providing a"
+                                " `latch_metadata.py` file in the workflow root.\nThis"
+                                " way it is not necessary to install dependencies or"
+                                " ensure that Snakemake inputs locally."
+                            ),
                             fg="red",
                         )
                         click.secho("\nExample ", fg="red", nl=False)
@@ -240,6 +253,28 @@ def __init__(
                 # name for snakemake
                 self.workflow_name = metadata._snakemake_metadata.name
 
+            else:
+                assert nf_script is not None
+
+                import latch.types.metadata as metadata
+
+                meta = pkg_root / "latch_metadata" / "__init__.py"
+                if meta.exists():
+                    click.echo(f"Using metadata file {click.style(meta, italic=True)}")
+                    import_module_by_path(meta)
+
+                if metadata._nextflow_metadata is None:
+                    click.secho(
+                        dedent(
+                            """Make sure a `latch_metadata.py` file exists in the
+                        nextflow project root.""",
+                        ),
+                        fg="red",
+                    )
+                    raise click.exceptions.Exit(1)
+
+                self.workflow_name = metadata._nextflow_metadata.name
+
             version_file = self.pkg_root / "version"
             try:
                 self.version = version_file.read_text()
@@ -258,8 +293,10 @@ def __init__(
 
             if self.nucleus_check_version(self.version, self.workflow_name):
                 click.secho(
-                    f"\nVersion ({self.version}) already exists."
-                    " Make sure that you've saved any changes you made.",
+                    (
+                        f"\nVersion ({self.version}) already exists."
+                        " Make sure that you've saved any changes you made."
+                    ),
                     fg="red",
                     bold=True,
                 )
@@ -298,7 +335,8 @@ def __init__(
                 )
                 self.ssh_client = ssh_client
 
-                def _patched_connect(self): ...
+                def _patched_connect(self):
+                    ...
 
                 def _patched_create_paramiko_client(self, base_url):
                     self.ssh_client = ssh_client

latch_cli/docker_utils/__init__.py

@@ -37,6 +37,8 @@ def get_prologue(
 ) -> List[str]:
     if wf_type == WorkflowType.snakemake:
         library_name = '"latch[snakemake]"'
+    elif wf_type == WorkflowType.nextflow:
+        library_name = '"latch[nextflow]"'
     else:
         library_name = "latch"
     return [
@@ -80,6 +82,14 @@ def get_epilogue(wf_type: WorkflowType = WorkflowType.latchbiosdk) -> List[str]:
             "# DO NOT CHANGE",
             "copy .latch/snakemake_jit_entrypoint.py /root/snakemake_jit_entrypoint.py",
         ]
+    elif wf_type == WorkflowType.nextflow:
+        cmds += [
+            "",
+            "# Latch nextflow workflow entrypoint",
+            "# DO NOT CHANGE",
+            "copy .latch/latch-nextflow /root/latch-nextflow",
+            "copy .latch/nextflow_jit_entrypoint.py /root/nextflow_jit_entrypoint.py",
+        ]
 
     cmds += [
         "",
@@ -248,7 +258,8 @@ def infer_commands(pkg_root: Path) -> List[DockerCmdBlock]:
 
                 has_buildable_pyproject = True
                 break
-    except FileNotFoundError: ...
+    except FileNotFoundError:
+        ...
 
     # from https://peps.python.org/pep-0518/ and https://peps.python.org/pep-0621/
     if has_setup_py or has_buildable_pyproject:

latch_cli/main.py

@@ -176,6 +176,10 @@ def dockerfile(pkg_root: str, snakemake: bool = False):
         "Whether or not to cache snakemake tasks. Ignored if --snakefile is not"
         " provided."
     ),
+    "--nf-script",
+    type=click.Path(exists=True, dir_okay=False, path_type=Path),
+    default=None,
+    help="Path to a nextflow script to register.",
 )
 @requires_login
 def register(
@@ -186,6 +190,7 @@ def register(
     yes: bool,
     snakefile: Optional[Path],
     cache_tasks: bool,
+    nf_script: Optional[Path],
 ):
     """Register local workflow code to Latch.
 
@@ -205,6 +210,7 @@ def register(
         remote=remote,
         skip_confirmation=yes,
         snakefile=snakefile,
+        nf_script=nf_script,
         progress_plain=(docker_progress == "auto" and not sys.stdout.isatty())
         or docker_progress == "plain",
         use_new_centromere=use_new_centromere,
@@ -523,8 +529,10 @@ def get_params(wf_name: Union[str, None], version: Union[str, None] = None):
     if version is None:
         version = "latest"
     click.secho(
-        f"Successfully generated python param map named {wf_name}.params.py with"
-        f" version {version}\n Run `latch launch {wf_name}.params.py` to launch it.",
+        (
+            f"Successfully generated python param map named {wf_name}.params.py with"
+            f" version {version}\n Run `latch launch {wf_name}.params.py` to launch it."
+        ),
         fg="green",
     )