diff --git a/pyproject.toml b/pyproject.toml
index 07f1a298..7b706a76 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "setuptools-scm", "cython"]
+requires = ["setuptools", "setuptools-scm"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -24,12 +24,6 @@ dependencies = [
   "pyyaml",
   "xarray[io]",
 
-  # Workflow Planner
-  "jinja2",
-  "networkx",
-  "printree",
-  "pyvis",
-
   # Numerics
   "numexpr",
   "numpy",
@@ -67,13 +61,11 @@ generate-rupture-propagation = "workflow.scripts.generate_rupture_propagation:ap
 copy-domain-parameters = "workflow.scripts.copy_velocity_model_parameters:app"
 create-e3d-par = "workflow.scripts.create_e3d_par:app"
 generate-stoch = "workflow.scripts.generate_stoch:app"
-merge-ts = "workflow.scripts.merge_ts:app"
 hf-sim = "workflow.scripts.hf_sim:app"
 bb-sim = "workflow.scripts.bb_sim:app"
 im-calc = "workflow.scripts.im_calc:app"
 check-srf = "workflow.scripts.check_srf:app"
 check-domain = "workflow.scripts.check_domain:app"
-plan-workflow = "workflow.scripts.plan_workflow:app"
 gcmt-auto-simulate = "workflow.scripts.gcmt_auto_simulate:app"
 import-realisation = "workflow.scripts.import_realisation:app"
 lf-to-xarray = "workflow.scripts.lf_to_xarray:app"
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 9a458991..00000000
--- a/setup.py
+++ /dev/null
@@ -1,14 +0,0 @@
-from Cython.Build import cythonize
-from setuptools import Extension, setup
-
-extensions = [
-    Extension(
-        "workflow.scripts.merge_ts_loop",
-        ["workflow/scripts/merge_ts_loop.pyx"],
-    ),
-]
-
-setup(
-    name="workflow",
-    ext_modules=cythonize(extensions),
-)
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 066f8956..4b466473 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -22,7 +22,6 @@
     import_realisation,
     lf_to_xarray,
     nshm2022_to_realisation,
-    plan_workflow,
     realisation_to_srf,
 )
 
@@ -47,7 +46,6 @@
         im_calc,
         import_realisation,
         nshm2022_to_realisation,
-        plan_workflow,
         realisation_to_srf,
     ],
 )
diff --git a/wiki/Stages.md b/wiki/Stages.md
index af14ecaf..49a54d40 100644
--- a/wiki/Stages.md
+++ b/wiki/Stages.md
@@ -219,20 +219,6 @@ Can be run in the cybershake container. Can also be run from your own computer u
 See the output of `create-e3d-par --help` or [create_e3d_par.py](https://github.com/ucgmsim/workflow/blob/pegasus/workflow/scripts/create_e3d_par.py).
 See our description of the [EMOD3D Parameters](https://wiki.canterbury.ac.nz/pages/viewpage.action?pageId=100794983) for documentation on the EMOD3D parameter file format.
 
-## Merge Timeslices
-### Description
-Merge the output timeslice files of EMOD3D.
-### Inputs
-1. A directory containing EMOD3D timeslice files.
-### Outputs
-1. A merged output timeslice file.
-### Environment
-Can be run in the cybershake container. Can also be run from your own computer using the `merge-ts` command which is installed after running `pip install workflow@git+https://github.com/ucgmsim/workflow`.
-### Usage
-`merge_ts XYTS_DIRECTORY XYTS_DIRECTORY/output.e3d`
-### For More Help
-See the output of `merge-ts --help` or [merge_ts.py](https://github.com/ucgmsim/workflow/blob/pegasus/merge_ts/merge_ts.py).
-
 ## Create Simulation Video
 ### Description
 Create a simulation video from the low frequency simulation output.
diff --git a/workflow/__init__.py b/workflow/__init__.py
index 26c75bf3..a8e2b769 100644
--- a/workflow/__init__.py
+++ b/workflow/__init__.py
@@ -70,7 +70,6 @@
 | EMOD3D                        | See below.                                            |
 | High Frequency Simulation     | `workflow.scripts.hf_sim`                             |
 | Broadband Simulation          | `workflow.scripts.bb_sim`                             |
-| Merge Timeslices              | `merge_ts.merge_ts`                                   |
 | Create Simulation Video       | `workflow.scripts.plot_ts`                            |
 | Intensity Measure Calculation | `workflow.scripts.im_calc`                            |
 
diff --git a/workflow/scripts/merge_ts.py b/workflow/scripts/merge_ts.py
deleted file mode 100644
index 3e37f82e..00000000
--- a/workflow/scripts/merge_ts.py
+++ /dev/null
@@ -1,288 +0,0 @@
-#!/usr/bin/env python3
-"""Merge EMOD3D Timeslices.
-
-Description
------------
-Merge the output timeslice files of EMOD3D.
-
-Inputs
-------
-1. A directory containing EMOD3D timeslice files.
-
-Outputs
--------
-1. A merged output timeslice file.
-
-Environment
------------
-Can be run in the cybershake container. Can also be run from your own computer using the `merge-ts` command which is installed after running `pip install workflow@git+https://github.com/ucgmsim/workflow`.
-
-Usage
------
-`merge_ts XYTS_DIRECTORY XYTS_DIRECTORY/output.e3d`
-
-For More Help
--------------
-See the output of `merge-ts --help`.
-"""
-
-import os
-from pathlib import Path
-from typing import Annotated
-
-import numpy as np
-import tqdm
-import typer
-import xarray as xr
-
-from qcore import cli, coordinates, xyts
-from workflow.scripts import merge_ts_loop  # type: ignore
-
-app = typer.Typer()
-
-
-def merge_ts_xyts(
-    component_xyts_directory: Annotated[
-        Path,
-        typer.Argument(
-            dir_okay=True,
-            file_okay=False,
-            exists=True,
-            readable=True,
-        ),
-    ],
-    output: Annotated[
-        Path,
-        typer.Argument(dir_okay=False, writable=True),
-    ],
-    glob_pattern: str = "*xyts-*.e3d",
-) -> None:
-    """Merge XYTS files.
-
-    Parameters
-    ----------
-    component_xyts_directory : Path
-        The input xyts directory containing files to merge.
-    output : Path
-        The output xyts file.
-    glob_pattern : str, optional
-        Set a custom glob pattern for merging the xyts files, by default "*xyts-*.e3d".
-    """
-    component_xyts_files = sorted(
-        [
-            xyts.XYTSFile(
-                xyts_file_path, proc_local_file=True, meta_only=True, round_dt=False
-            )
-            for xyts_file_path in component_xyts_directory.glob(glob_pattern)
-        ],
-        key=lambda xyts_file: (xyts_file.y0, xyts_file.x0),
-    )
-    top_left = component_xyts_files[0]
-    merged_ny = top_left.ny
-    merged_nt = top_left.nt
-
-    xyts_proc_header_size = 72
-
-    xyts_file_descriptors: list[int] = []
-    for xyts_file in component_xyts_files:
-        xyts_file_descriptor = os.open(xyts_file.xyts_path, os.O_RDONLY)
-        # Skip the header for each file descriptor
-        head_skip = os.lseek(xyts_file_descriptor, xyts_proc_header_size, os.SEEK_SET)
-        if head_skip != xyts_proc_header_size:
-            raise ValueError(
-                f"Failed to skip header for {xyts_file.xyts_path} at {head_skip}"
-            )
-        xyts_file_descriptors.append(xyts_file_descriptor)
-
-    # If output doesn't exist when we os.open it, we'll get an error.
-    output.touch()
-    merged_fd = os.open(output, os.O_WRONLY)
-    # The following type: ignores can be removed once qcore updates
-    xyts_header: bytes = (
-        top_left.x0.tobytes()  # type: ignore
-        + top_left.y0.tobytes()  # type: ignore
-        + top_left.z0.tobytes()  # type: ignore
-        + top_left.t0.tobytes()  # type: ignore
-        + top_left.nx.tobytes()  # type: ignore
-        + top_left.ny.tobytes()  # type: ignore
-        + top_left.nz.tobytes()  # type: ignore
-        + top_left.nt.tobytes()  # type: ignore
-        + top_left.dx.tobytes()  # type: ignore
-        + top_left.dy.tobytes()  # type: ignore
-        + top_left.hh.tobytes()  # type: ignore
-        + top_left.dt.tobytes()  # type: ignore
-        + top_left.mrot.tobytes()  # type: ignore
-        + top_left.mlat.tobytes()  # type: ignore
-        + top_left.mlon.tobytes()  # type: ignore
-    )
-
-    written = os.write(merged_fd, xyts_header)
-    if written != len(xyts_header):
-        raise ValueError(
-            f"Failed to write header for {output} at {written} bytes written"
-        )
-
-    merge_ts_loop.merge_fds(
-        merged_fd,
-        xyts_file_descriptors,
-        merged_nt,
-        merged_ny,
-        [f.local_nx for f in component_xyts_files],
-        [f.local_ny for f in component_xyts_files],
-        [f.y0 for f in component_xyts_files],
-    )
-
-    for xyts_file_descriptor in xyts_file_descriptors:
-        os.close(xyts_file_descriptor)
-
-    os.close(merged_fd)
-
-
-@cli.from_docstring(app, name="hdf5")  # type: ignore
-def merge_ts_hdf5(
-    component_xyts_directory: Annotated[
-        Path,
-        typer.Argument(
-            dir_okay=True,
-            file_okay=False,
-            exists=True,
-            readable=True,
-        ),
-    ],
-    output: Annotated[
-        Path,
-        typer.Argument(dir_okay=False, writable=True),
-    ],
-    glob_pattern: str = "*xyts-*.e3d",
-    complevel: int = 4,
-) -> None:
-    """Merge XYTS files.
-
-    Parameters
-    ----------
-    component_xyts_directory : Path
-        The input xyts directory containing files to merge.
-    output : Path
-        The output xyts file.
-    glob_pattern : str, optional
-        Set a custom glob pattern for merging the xyts files, by default "*xyts-*.e3d".
-    complevel : int, optional
-        Set the compression level for the output HDF5 file. Range
-        between 1-9 (9 being the highest level of compression).
-        Defaults to 4.
-    """
-    component_xyts_files = sorted(
-        [
-            xyts.XYTSFile(
-                xyts_file_path, proc_local_file=True, meta_only=True, round_dt=False
-            )
-            for xyts_file_path in component_xyts_directory.glob(glob_pattern)
-        ],
-        key=lambda xyts_file: (xyts_file.y0, xyts_file.x0),
-    )
-    top_left = component_xyts_files[0]
-    nt = top_left.nt
-    nx = top_left.nx
-    ny = top_left.ny
-    components = 3
-
-    xyts_proc_header_size = 72
-
-    waveform_data = np.empty((nt, ny, nx), dtype=np.uint16)
-    for xyts_file in tqdm.tqdm(component_xyts_files, unit="files"):
-        x0 = xyts_file.x0
-        y0 = xyts_file.y0
-        x1 = x0 + xyts_file.local_nx
-        y1 = y0 + xyts_file.local_ny
-        data = np.fromfile(
-            xyts_file.xyts_path, dtype=np.float32, offset=xyts_proc_header_size
-        ).reshape((nt, components, xyts_file.local_ny, xyts_file.local_nx))
-        magnitude = np.linalg.norm(data, axis=1) / 0.1
-        np.round(magnitude, out=magnitude)
-        waveform_data[:, y0:y1, x0:x1] = magnitude.astype(np.uint16)
-
-    proj = coordinates.SphericalProjection(
-        mlon=top_left.mlon, mlat=top_left.mlat, mrot=top_left.mrot
-    )
-    dx = top_left.hh
-    dt = top_left.dt
-    y, x = np.meshgrid(
-        np.arange(ny, dtype=np.float64), np.arange(nx, dtype=np.float64), indexing="ij"
-    )
-    lat, lon = proj.inverse(x.flatten(), y.flatten()).T
-    lat = lat.reshape(y.shape)
-    lon = lon.reshape(y.shape)
-    time = np.arange(nt) * dt
-    dset = xr.Dataset(
-        {
-            "waveform": (("time", "y", "x"), waveform_data),
-        },
-        coords={
-            "time": ("time", time),
-            "y": ("y", np.arange(ny)),
-            "x": ("x", np.arange(nx)),
-            "latitude": (("y", "x"), lat),
-            "longitude": (("y", "x"), lon),
-        },
-        attrs={
-            "dx": dx,
-            "dy": dx,
-            "dt": dt,
-            "mlon": top_left.mlon,
-            "mlat": top_left.mlat,
-            "mrot": top_left.mrot,
-        },
-    )
-
-    dset["waveform"].attrs.update(
-        {
-            "scale_factor": 0.1,
-            "add_offset": 0.0,
-            "units": "cm/s",
-            "_FillValue": -9999,
-        }
-    )
-
-    dset.to_netcdf(
-        output,
-        engine="h5netcdf",
-        encoding={
-            "waveform": {
-                "dtype": "int16",
-                "compression": "zlib",
-                "complevel": complevel,
-                "shuffle": True,
-            }
-        },
-    )
-
-
-@cli.from_docstring(app, name="xyts")  # type: ignore
-def merge_ts(
-    component_xyts_directory: Annotated[
-        Path,
-        typer.Argument(
-            dir_okay=True,
-            file_okay=False,
-            exists=True,
-            readable=True,
-        ),
-    ],
-    output: Annotated[
-        Path,
-        typer.Argument(dir_okay=False, writable=True),
-    ],
-    glob_pattern: str = "*xyts-*.e3d",
-) -> None:
-    """Merge XYTS files.
-
-    Parameters
-    ----------
-    component_xyts_directory : Path
-        The input xyts directory containing files to merge.
-    output : Path
-        The output xyts file.
-    glob_pattern : str, optional
-        Set a custom glob pattern for merging the xyts files, by default "*xyts-*.e3d".
-    """
-    merge_ts_xyts(component_xyts_directory, output, glob_pattern)
diff --git a/workflow/scripts/merge_ts_loop.pyx b/workflow/scripts/merge_ts_loop.pyx
deleted file mode 100644
index d83a57c3..00000000
--- a/workflow/scripts/merge_ts_loop.pyx
+++ /dev/null
@@ -1,79 +0,0 @@
-import os
-
-import cython
-
-from libc.stdlib cimport free, malloc
-
-cdef extern from "sys/types.h":
-    ctypedef long off_t
-cdef extern from "sys/sendfile.h":
-    ssize_t sendfile(int out_fd, int in_fd, off_t * offset, size_t count)
-
-def merge_fds(
-    int merged_fd, _component_xyts_files, int merged_nt, int merged_ny, _local_nxs, _local_nys, _y0s
-):
-    ''' Merge a list of XYTS files by copying their values in order.
-
-    To merge the files we copy the velocity values in each component, for each
-    timestep, in the order they would fit in the merged domain. That is if four
-    files tile the domain like so:
-
-            ┌───────────┬──────────┐
-            │***********│##########│
-            │!!!!!!!!!!!│++++++++++│
-            │    f1     │    f2    │
-            │           │          │
-            ├───────────┼──────────┤
-            │$$$$$$$$$$$│%%%%%%%%%%│
-            │           │          │
-            │    f3     │    f4    │
-            │           │          │
-            │           │          │
-            └───────────┴──────────┘
-
-    Then they are concatenated in the output domain as:
-
-    ***********##########!!!!!!!!!!!++++++++++ ... $$$$$$$$$$$%%%%%%%%%%
-
-    It is assumed _component_xyts_files is a list of xyts files sorted by their
-    top left corner.
-    '''
-    cdef int float_size, cur_timestep, cur_component, cur_y, i, y0, local_ny, local_nx, xyts_fd, n_files
-    cdef int *component_xyts_files, *local_nxs, *local_nys, *y0s
-
-    n_files = len(_component_xyts_files)
-
-    # The lists _component_xyts_files, ... are CPython lists.
-    # If we access these inside our copying loop everything becomes very slow
-    # because we need to go to the Python interpreter. So we first copy each
-    # list into an equivalent C list.
-    component_xyts_files = <int *> malloc(len(_component_xyts_files) * cython.sizeof(int))
-    local_nxs = <int *> malloc(len(_local_nxs) * cython.sizeof(int))
-    local_nys = <int *> malloc(len(_local_nys) * cython.sizeof(int))
-    y0s = <int *> malloc(len(_y0s) * cython.sizeof(int))
-    # NOTE: we cannot use memcpy() here because CPython lists are not continuous
-    # chunks of memory as they are in C.
-    for i in range(len(_component_xyts_files)):
-        component_xyts_files[i] = _component_xyts_files[i]
-        local_nxs[i] = _local_nxs[i]
-        local_nys[i] = _local_nys[i]
-        y0s[i] = _y0s[i]
-    for cur_timestep in range(merged_nt):
-        for cur_component in range(3):  # for each component
-            for cur_y in range(merged_ny):
-                for i in range(n_files):
-                    y0 = y0s[i]
-                    local_ny = local_nys[i]
-                    local_nx = local_nxs[i]
-                    xyts_fd = component_xyts_files[i]
-                    if y0 > cur_y:
-                        break
-                    if cur_y >= y0 + local_ny:
-                        continue
-                    # By passing NULL as the offset, sendfile() will read from
-                    # the current position in xyts_fd
-                    sendfile(merged_fd, xyts_fd, NULL, local_nx * 4)
-    free(component_xyts_files)
-    free(local_nxs)
-    free(local_nys)
-    free(y0s)
diff --git a/workflow/scripts/plan_workflow.py b/workflow/scripts/plan_workflow.py
deleted file mode 100644
index 27df5fb5..00000000
--- a/workflow/scripts/plan_workflow.py
+++ /dev/null
@@ -1,825 +0,0 @@
-"""Create a Cylc workflow plan from a list of goals and stages to exclude.
-
-This is the starting point for most workflow usages, and can be used
-to generate a base Cylc workflow to modify and extend.
-"""
-
-import dataclasses
-import tempfile
-from collections.abc import Iterable
-from enum import StrEnum
-from pathlib import Path, PurePath
-from typing import Annotated, Any, Optional, Self
-
-import jinja2
-import networkx as nx
-import printree
-import tqdm
-import typer
-from pyvis.network import Network
-
-from qcore import cli
-from workflow import realisations
-from workflow.defaults import DefaultsVersion
-
-app = typer.Typer()
-
-
-class WorkflowTarget(StrEnum):
-    """Enumeration of possible workflow targets."""
-
-    NeSI = "nesi"
-    Hypocentre = "hypocentre"
-
-
-class StageIdentifier(StrEnum):
-    """Valid stage identifier in the workflow plan."""
-
-    CopyInput = "copy_input"
-    Archive = "archive"
-    GCMTToRealisation = "gcmt_to_realisation"
-    DomainGeneration = "generate_velocity_model_parameters"
-    VelocityModelGeneration = "generate_velocity_model"
-    StationSelection = "generate_station_coordinates"
-    ModelCoordinates = "write_model_coordinates"
-    SRFGeneration = "realisation_to_srf"
-    CheckSRF = "check_srf"
-    CopyDomainParameters = "copy_domain_parameters"
-    EMOD3DParameters = "create_e3d_par"
-    CheckDomain = "check_domain"
-    StochGeneration = "generate_stoch"
-    HighFrequency = "hf_sim"
-    LowFrequency = "emod3d"
-    Broadband = "bb_sim"
-    IntensityMeasureCalculation = "im_calc"
-    MergeTimeslices = "merge_ts"
-    NSHMToRealisation = "nshm_to_realisation"
-
-
-class Source(StrEnum):
-    """Realisation source options."""
-
-    GCMT = "gcmt"
-    NSHM = "nshm"
-
-
-class GroupIdentifier(StrEnum):
-    """Group identifiers to use to bulk target or exclude in workflow planning."""
-
-    Preprocessing = "preprocessing"
-    """Alias for all preprocessing stages."""
-    HighFrequency = "high_frequency"
-    """Alias for the high frequency workflow."""
-    LowFrequency = "low_frequency"
-    """Alias for the low frequency workflow."""
-    Domain = "domain"
-
-
-GROUP_STAGES = {
-    GroupIdentifier.Preprocessing: {
-        StageIdentifier.DomainGeneration,
-        StageIdentifier.VelocityModelGeneration,
-        StageIdentifier.StationSelection,
-        StageIdentifier.ModelCoordinates,
-        StageIdentifier.SRFGeneration,
-        StageIdentifier.EMOD3DParameters,
-        StageIdentifier.NSHMToRealisation,
-        StageIdentifier.GCMTToRealisation,
-        StageIdentifier.StochGeneration,
-        StageIdentifier.CopyDomainParameters,
-    },
-    GroupIdentifier.HighFrequency: {
-        StageIdentifier.HighFrequency,
-    },
-    GroupIdentifier.LowFrequency: {StageIdentifier.LowFrequency},
-    GroupIdentifier.Domain: {
-        StageIdentifier.VelocityModelGeneration,
-        StageIdentifier.StationSelection,
-        StageIdentifier.DomainGeneration,
-        StageIdentifier.CopyDomainParameters,
-        StageIdentifier.ModelCoordinates,
-    },
-}
-
-GROUP_GOALS = {
-    GroupIdentifier.Preprocessing: {
-        StageIdentifier.EMOD3DParameters,
-        StageIdentifier.StochGeneration,
-    },
-    GroupIdentifier.LowFrequency: {StageIdentifier.LowFrequency},
-    GroupIdentifier.HighFrequency: {StageIdentifier.HighFrequency},
-    GroupIdentifier.Domain: {
-        StageIdentifier.VelocityModelGeneration,
-        StageIdentifier.StationSelection,
-        StageIdentifier.ModelCoordinates,
-        StageIdentifier.CopyDomainParameters,
-    },
-}
-
-CONTAINER_PATHS = {
-    WorkflowTarget.NeSI: Path("/nesi/nobackup/nesi00213/containers/runner_latest.sif"),
-    WorkflowTarget.Hypocentre: Path("/mnt/hypo_scratch/containers/runner_latest.sif"),
-}
-
-EMOD3D_PATHS = {
-    WorkflowTarget.NeSI: Path(
-        "/nesi/project/nesi00213/opt/EMOD3D_cylc/tools/emod3d-mpi_v3.0.8"
-    ),
-    WorkflowTarget.Hypocentre: Path("/mnt/hypo_scratch/EMOD3D/tools/emod3d-mpi_v3.0.8"),
-}
-
-
-@dataclasses.dataclass
-class Stage:
-    """Representation of a workflow stage in the output Cylc file."""
-
-    identifier: StageIdentifier
-    """The stage identifier."""
-    event: str | None
-    """The event the stage is running for."""
-    sample: int | None
-    """The sample number of the realisation."""
-
-    @property
-    def parent(self) -> Self:  # numpydoc ignore=RT01
-        """Stage: the parent stage of this stage."""
-        return dataclasses.replace(self, sample=None)
-
-    @property
-    def directory(self) -> PurePath | None:  # numpydoc ignore=RT01
-        """PurePath: the directory for this stage."""
-        if not self.event:
-            return None
-        directory = self.event
-        if self.sample:
-            directory += f"_{self.sample}"
-        return PurePath(directory)
-
-    @property
-    def outputs(self) -> set[PurePath]:  # numpydoc ignore=RT01
-        """set[PurePath]: the outputs for this stage."""
-        directory = self.directory
-        if not directory:
-            return set()
-        return {directory / output for output in stage_outputs(self.identifier)}
-
-    @property
-    def inputs(self) -> set[PurePath]:  # numpydoc ignore=RT01
-        """set[PurePath]: the inputs for this stage."""
-        directory = self.directory
-        if not self.event or not directory:
-            return set()
-        workflow_plan = realisation_workflow(self.event, self.sample)
-        try:
-            input_stages = list(workflow_plan.predecessors(self))
-            inputs = set()
-            for stage in input_stages:
-                inputs |= stage.outputs
-            return inputs
-        except nx.NetworkXError:
-            return set()
-
-    def __hash__(self) -> int:
-        """Hash the stage identifier, event and sample number.
-
-        Returns
-        -------
-        int
-            The hash of the stage.
-        """
-        return hash((self.identifier, self.event, self.sample))
-
-    def __str__(self) -> str:
-        """The string representation of the stage.
-
-        Returns
-        -------
-        str
-            The string representation of the stage."""
-        _str = str(self.identifier)
-        if self.event:
-            _str += f"_{self.event}"
-        if self.sample:
-            _str += f"_{self.sample}"
-        return _str
-
-
-def stage_config_outputs(identifier: StageIdentifier) -> set[str]:
-    """Get the realisation configuration outputs for a given stage.
-
-    Parameters
-    ----------
-    identifier : StageIdentifier
-        The stage to get outputs for.
-
-
-    Returns
-    -------
-    set[str]
-        The output config sections for this stage.
-    """
-    output_dictionary = {
-        StageIdentifier.NSHMToRealisation: {
-            realisations.SourceConfig._config_key,
-            realisations.RupturePropagationConfig._config_key,
-            realisations.RealisationMetadata._config_key,
-        },
-        StageIdentifier.GCMTToRealisation: {
-            realisations.SourceConfig._config_key,
-            realisations.RupturePropagationConfig._config_key,
-            realisations.RealisationMetadata._config_key,
-        },
-        StageIdentifier.EMOD3DParameters: {realisations.EMOD3DParameters._config_key},
-        StageIdentifier.Broadband: {realisations.BroadbandParameters._config_key},
-        StageIdentifier.VelocityModelGeneration: {
-            realisations.VelocityModelParameters._config_key
-        },
-        StageIdentifier.HighFrequency: {realisations.HFConfig._config_key},
-        StageIdentifier.IntensityMeasureCalculation: {
-            realisations.IntensityMeasureCalculationParameters._config_key
-        },
-        StageIdentifier.CopyDomainParameters: {
-            realisations.VelocityModelParameters._config_key,
-            realisations.DomainParameters._config_key,
-        },
-        StageIdentifier.DomainGeneration: {
-            realisations.VelocityModelParameters._config_key,
-            realisations.DomainParameters._config_key,
-        },
-        StageIdentifier.SRFGeneration: {realisations.SRFConfig._config_key},
-        StageIdentifier.StochGeneration: {realisations.HFConfig._config_key},
-    }
-    return output_dictionary.get(identifier, set())
-
-
-def stage_outputs(
-    identifier: StageIdentifier, include_config_outputs: bool = True
-) -> set[PurePath]:
-    """Return a set of stage outputs for the given stage identifier.
-
-    Parameters
-    ----------
-    identifier : StageIdentifier
-        The stage identifier to get outputs for.
-    include_config_outputs : bool, optional
-        Whether to include configuration outputs (default is True).
-
-    Returns
-    -------
-    set[PurePath]
-        A set of output paths for the stage.
-    """
-    output_dictionary = {
-        StageIdentifier.SRFGeneration: {
-            PurePath("realisation.srf"),
-        },
-        StageIdentifier.ModelCoordinates: {
-            PurePath("model") / "model_params",
-            PurePath("model") / "grid_file",
-        },
-        StageIdentifier.StationSelection: {
-            PurePath("stations") / "stations.ll",
-            PurePath("stations") / "stations.statcords",
-        },
-        StageIdentifier.VelocityModelGeneration: {
-            PurePath("Velocity_Model") / "rho3dfile.d",
-            PurePath("Velocity_Model") / "vp3dfile.p",
-            PurePath("Velocity_Model") / "vs3dfile.s",
-            PurePath("Velocity_Model") / "in_basin_mask.b",
-        },
-        StageIdentifier.EMOD3DParameters: {
-            PurePath("LF"),
-            PurePath("LF") / "e3d.par",
-        },
-        StageIdentifier.LowFrequency: {PurePath("LF")},
-        StageIdentifier.StochGeneration: {
-            PurePath("realisation.stoch"),
-        },
-        StageIdentifier.HighFrequency: {PurePath("realisation.hf")},
-        StageIdentifier.Broadband: {PurePath("realisation.bb")},
-        StageIdentifier.IntensityMeasureCalculation: {
-            PurePath("intensity_measures.parquet")
-        },
-        StageIdentifier.MergeTimeslices: {PurePath("LF") / "OutBin" / "output.e3d"},
-    }
-    file_outputs = output_dictionary.get(identifier, set())
-    if include_config_outputs:
-        for output in stage_config_outputs(identifier):
-            file_outputs.add(PurePath("realisation.json") / output)
-
-    return file_outputs
-
-
-def realisation_workflow(event: str, sample: int | None) -> nx.DiGraph:
-    """Add a realisation to a workflow plan.
-
-    Adds all stages for the realisation to run, and links to event
-    stages for shared resources (i.e. the velocity model).
-
-    Parameters
-    ----------
-    event : str
-        The event to add.
-    sample : int or None
-        The sample number (or None, if the original event).
-
-    Returns
-    -------
-    nx.DiGraph
-        The workflow plan with the added realisation.
-    """
-    requires_base = [
-        StageIdentifier.SRFGeneration,
-        StageIdentifier.StochGeneration,
-        StageIdentifier.CheckSRF,
-        StageIdentifier.VelocityModelGeneration,
-        StageIdentifier.DomainGeneration,
-        StageIdentifier.EMOD3DParameters,
-        StageIdentifier.IntensityMeasureCalculation,
-        StageIdentifier.HighFrequency,
-        StageIdentifier.Broadband,
-    ]
-    requires_domain = [
-        StageIdentifier.ModelCoordinates,
-        StageIdentifier.Broadband,
-        StageIdentifier.StationSelection,
-        StageIdentifier.CheckDomain,
-        StageIdentifier.CopyDomainParameters,
-        StageIdentifier.VelocityModelGeneration,
-        StageIdentifier.HighFrequency,
-        StageIdentifier.EMOD3DParameters,
-    ]
-    workflow_plan = nx.from_dict_of_lists(
-        {
-            Stage(StageIdentifier.NSHMToRealisation, event, sample): [
-                Stage(id, event, sample) for id in requires_base
-            ],
-            Stage(StageIdentifier.GCMTToRealisation, event, sample): [
-                Stage(id, event, sample) for id in requires_base
-            ],
-            Stage(StageIdentifier.SRFGeneration, event, sample): [
-                Stage(StageIdentifier.CheckSRF, event, sample),
-                Stage(StageIdentifier.LowFrequency, event, sample),
-            ],
-            Stage(StageIdentifier.CheckSRF, event, sample): [
-                Stage(StageIdentifier.StochGeneration, event, sample),
-                Stage(StageIdentifier.EMOD3DParameters, event, sample),
-            ],
-            Stage(StageIdentifier.VelocityModelGeneration, event, None): [
-                Stage(StageIdentifier.EMOD3DParameters, event, sample),
-                Stage(StageIdentifier.HighFrequency, event, sample),
-                Stage(
-                    StageIdentifier.Broadband, event, sample
-                ),  # This is a transitive dependency, but is useful for determining stage inputs
-            ],
-            Stage(StageIdentifier.StationSelection, event, None): [
-                Stage(StageIdentifier.EMOD3DParameters, event, sample),
-                Stage(StageIdentifier.HighFrequency, event, sample),
-            ],
-            Stage(StageIdentifier.ModelCoordinates, event, None): [
-                Stage(StageIdentifier.EMOD3DParameters, event, sample)
-            ],
-            Stage(StageIdentifier.EMOD3DParameters, event, sample): [
-                Stage(StageIdentifier.CheckDomain, event, sample),
-                Stage(StageIdentifier.LowFrequency, event, sample),
-            ],
-            Stage(StageIdentifier.CheckDomain, event, sample): [
-                Stage(StageIdentifier.LowFrequency, event, sample)
-            ],
-            Stage(StageIdentifier.LowFrequency, event, sample): [
-                Stage(StageIdentifier.Broadband, event, sample),
-                Stage(StageIdentifier.MergeTimeslices, event, sample),
-            ],
-            Stage(StageIdentifier.StochGeneration, event, sample): [
-                Stage(StageIdentifier.HighFrequency, event, sample)
-            ],
-            Stage(StageIdentifier.HighFrequency, event, sample): [
-                Stage(StageIdentifier.Broadband, event, sample)
-            ],
-            Stage(StageIdentifier.Broadband, event, sample): [
-                Stage(StageIdentifier.IntensityMeasureCalculation, event, sample)
-            ],
-        },
-        create_using=nx.DiGraph,
-    )
-    if not sample:
-        workflow_plan.add_edges_from(
-            [
-                (
-                    Stage(StageIdentifier.NSHMToRealisation, event, sample),
-                    Stage(StageIdentifier.DomainGeneration, event, sample),
-                ),
-                (
-                    Stage(StageIdentifier.GCMTToRealisation, event, sample),
-                    Stage(StageIdentifier.DomainGeneration, event, sample),
-                ),
-                (
-                    Stage(StageIdentifier.DomainGeneration, event, sample),
-                    Stage(StageIdentifier.EMOD3DParameters, event, sample),
-                ),
-                (
-                    Stage(StageIdentifier.DomainGeneration, event, sample),
-                    Stage(StageIdentifier.VelocityModelGeneration, event, sample),
-                ),
-                (
-                    Stage(StageIdentifier.DomainGeneration, event, sample),
-                    Stage(StageIdentifier.StationSelection, event, sample),
-                ),
-                (
-                    Stage(StageIdentifier.DomainGeneration, event, sample),
-                    Stage(StageIdentifier.ModelCoordinates, event, sample),
-                ),
-            ]
-        )
-        workflow_plan.add_edges_from(
-            [
-                (
-                    Stage(StageIdentifier.DomainGeneration, event, sample),
-                    Stage(id, event, sample),
-                )
-                for id in requires_domain
-            ]
-        )
-    else:
-        workflow_plan.add_edges_from(
-            [
-                (
-                    Stage(StageIdentifier.DomainGeneration, event, None),
-                    Stage(StageIdentifier.CopyDomainParameters, event, sample),
-                ),
-            ]
-        )
-        workflow_plan.add_edges_from(
-            [
-                (
-                    Stage(StageIdentifier.CopyDomainParameters, event, sample),
-                    Stage(id, event, sample),
-                )
-                for id in requires_domain
-                if id != StageIdentifier.CopyDomainParameters
-            ]
-        )
-    return workflow_plan
-
-
-def create_abstract_workflow_plan(
-    realisations: set[tuple[str, int | None]],
-    goals: Iterable[StageIdentifier],
-    excluding: Iterable[StageIdentifier],
-) -> nx.DiGraph:
-    """Create an abstract workflow graph from a list of goals and excluded stages.
-
-    Parameters
-    ----------
-    realisations : set[tuple[str, int | None]]
-        The realisations to generate the workflow for.
-    goals : Iterable[StageIdentifier]
-        The goal stages for the workflow.
-    excluding : Iterable[StageIdentifier]
-        The excluded stages for the workflow.
-
-    Returns
-    -------
-    nx.DiGraph
-        A abstract workflow plan. This workflow plan contains only
-        included stages that are required to reach the goals. If two
-        workflow stages depend on each other only through paths
-        consisting entirely of excluded nodes, then they are adjacent
-        directly in the abstract plan by edges.
-    """
-
-    excluding_stages = {
-        Stage(excluded, *realisation)
-        for excluded in excluding
-        for realisation in realisations
-    }
-
-    output_graph = nx.DiGraph()
-    realisation_iteration = (
-        realisations if len(realisations) < 100 else tqdm.tqdm(realisations)
-    )
-
-    for event, realisation in realisation_iteration:
-        workflow_plan = realisation_workflow(event, realisation)
-        workflow_plan = nx.transitive_closure_dag(workflow_plan)
-
-        for goal in goals:
-            reduced_graph = nx.transitive_reduction(
-                workflow_plan.subgraph(
-                    (
-                        set(workflow_plan.predecessors(Stage(goal, *realisation)))
-                        | {Stage(goal, *realisation)}
-                    )
-                    - excluding_stages
-                )
-            )
-            output_graph.update(
-                edges=reduced_graph.edges(), nodes=reduced_graph.nodes()
-            )
-
-    roots = [node for node, degree in output_graph.in_degree() if degree == 0]
-    ends = [node for node, degree in output_graph.out_degree() if degree == 0]
-    copy_input_stage = Stage(StageIdentifier.CopyInput, "", None)
-    archive_output_stage = Stage(StageIdentifier.Archive, "", None)
-
-    output_graph.add_node(copy_input_stage)
-    output_graph.add_node(archive_output_stage)
-    for root in roots:
-        output_graph.add_edge(copy_input_stage, root)
-    for end in ends:
-        output_graph.add_edge(end, archive_output_stage)
-    return output_graph
-
-
-def pyvis_graph(workflow_plan: nx.DiGraph) -> Network:
-    """Convert a workflow plan into a pyvis diagram for visualisation.
-
-    Parameters
-    ----------
-    workflow_plan : nx.DiGraph
-        The workflow plan to visualise.
-
-
-    Returns
-    -------
-    Network
-        A pyvis rendering for this workflow plan.
-    """
-    network = Network(
-        width="100%", height="1500px", directed=True, layout="hierarchical"
-    )
-    network.show_buttons(filter_=["physics"])
-    roots = [node for node, degree in workflow_plan.in_degree() if degree == 0]
-    reversed_workflow = workflow_plan.reverse()
-    stage: Stage
-    for stage in workflow_plan.nodes():
-        network.add_node(
-            str(stage),
-            group=f"{stage.event}_{stage.sample or ''}",
-            size=20,
-            level=max(
-                (
-                    len(path) - 1
-                    for root in roots
-                    for path in nx.all_simple_paths(reversed_workflow, stage, root)
-                ),
-                default=0,
-            ),
-        )
-    for stage, next_stage in workflow_plan.edges():
-        network.add_edge(str(stage), str(next_stage))
-    return network
-
-
-def parse_realisation(realisation_id: str) -> set[tuple[str, int | None]]:
-    """Parse a realisation identifier string from the command line into a realisation identifier.
-
-    Parameters
-    ----------
-    realisation_id : str
-        The realisation identifier string to parse.
-
-    Returns
-    -------
-    tuple[str, int | None]
-        The parsed realisation event and sample number.
-    """
-    try:
-        index = realisation_id.rindex(":")
-        event, num_samples = realisation_id[:index], realisation_id[index + 1 :]
-
-        return {(event, sample or None) for sample in range(int(num_samples))}
-    except ValueError:
-        return {(realisation_id, None)}
-
-
-def build_filetree(root_path: PurePath, files: set[PurePath]) -> dict[str, Any]:
-    """Build a file tree from a set of file paths.
-
-    Parameters
-    ----------
-    root_path : PurePath
-        The root path for the file tree.
-    files : set[PurePath]
-        The set of files to construct a tree for.
-
-
-    Returns
-    -------
-    dict[str, Any]
-        A file tree.
-    """
-    file_descriptions = {
-        "realisation.srf": "Contains the slip model for the realisation.",
-        "model_params": "Parameters for the model used in the simulation.",
-        "grid_file": "Grid file for the model coordinates.",
-        "stations.ll": "Station coordinates (lat, lon) in the simulation domain.",
-        "stations.statcords": "Station coordinates (x, y) in the simulation domain.",
-        "rho3dfile.d": "3D density model file.",
-        "vp3dfile.p": "3D P-wave velocity model file.",
-        "vs3dfile.s": "3D S-wave velocity model file.",
-        "in_basin_mask.b": "In-basin mask file for the velocity model.",
-        "LF": "Directory containing low frequency simulation files.",
-        "e3d.par": "EMOD3D parameter file.",
-        "realisation.stoch": "Stochastic file for the realisation.",
-        "realisation.hf": "High frequency waveform file for the realisation.",
-        "realisation.bb": "Broadband waveform file for the realisation.",
-        "intensity_measures.parquet": "Parquet file containing intensity measures.",
-        "animation.mp4": "Animation of the timeslices.",
-        "output.e3d": "Merged output file from the low frequency simulation.",
-    }
-    config_descriptions = {
-        realisations.RealisationMetadata._config_key: "Metadata for describing a realisation.",
-        realisations.SRFConfig._config_key: "Configuration for SRF generation.",
-        realisations.SourceConfig._config_key: "Configuration for defining sources.",
-        realisations.RupturePropagationConfig._config_key: "Configuration for rupture propagation.",
-        realisations.DomainParameters._config_key: "Parameters defining the spatial and temporal domain for simulation.",
-        realisations.VelocityModelParameters._config_key: "Parameters defining the velocity model.",
-        realisations.VelocityModel1D._config_key: "1D Velocity Model for SRF and HF.",
-        realisations.HFConfig._config_key: "High frequency simulation configuration.",
-        realisations.EMOD3DParameters._config_key: "Parameters for EMOD3D LF simulation.",
-        realisations.BroadbandParameters._config_key: "Parameters for broadband waveform merger.",
-        realisations.IntensityMeasureCalculationParameters._config_key: "Intensity measure calculation parameters.",
-    }
-    filetree: dict[str, Any] = {}
-
-    root = filetree
-    for part in root_path.parts:
-        root[part] = {}
-        root = root[part]
-
-    for file in sorted(files):
-        cur = root
-        for part in file.parts[:-1]:
-            if part not in cur:
-                cur[part] = {}
-            cur = cur[part]
-
-        if file.parent.name == "realisation.json":
-            cur[file.parts[-1]] = config_descriptions.get(file.name, {})
-        else:
-            cur[file.parts[-1]] = file_descriptions.get(file.name, {})
-
-    return filetree
-
-
-@cli.from_docstring(app)
-def plan_workflow(
-    realisation_ids: Annotated[list[str], typer.Argument()],
-    flow_file: Annotated[Path, typer.Argument(writable=True, dir_okay=False)],
-    goal: Annotated[
-        list[StageIdentifier],
-        typer.Option(default_factory=lambda: [], rich_help_panel="Planning Workflows"),
-    ],
-    group_goal: Annotated[
-        list[GroupIdentifier],
-        typer.Option(default_factory=lambda: [], rich_help_panel="Planning Workflows"),
-    ],
-    excluding: Annotated[
-        list[StageIdentifier],
-        typer.Option(default_factory=lambda: [], rich_help_panel="Planning Workflows"),
-    ],
-    excluding_group: Annotated[
-        list[GroupIdentifier],
-        typer.Option(default_factory=lambda: [], rich_help_panel="Planning Workflows"),
-    ],
-    archive: Annotated[
-        list[StageIdentifier],
-        typer.Option(
-            default_factory=lambda: [
-                StageIdentifier.Broadband,
-                StageIdentifier.IntensityMeasureCalculation,
-            ],
-            rich_help_panel="Archiving",
-        ),
-    ],
-    visualise: Annotated[
-        bool, typer.Option(rich_help_panel="Visualising Workflows")
-    ] = False,
-    show_required_files: Annotated[
-        bool, typer.Option(rich_help_panel="Visualising Workflows")
-    ] = True,
-    target_host: Annotated[
-        WorkflowTarget, typer.Option(rich_help_panel="Planning Workflows")
-    ] = WorkflowTarget.NeSI,
-    source: Annotated[Optional[Source], typer.Option(rich_help_panel="Sources")] = None,
-    defaults_version: Annotated[
-        Optional[DefaultsVersion], typer.Option(rich_help_panel="Sources")
-    ] = None,
-    container: Annotated[Optional[Path], typer.Option()] = None,
-    emod3d_path: Annotated[Optional[Path], typer.Option()] = None,
-) -> None:
-    """Plan and generate a Cylc workflow file for a number of realisations.
-
-    Parameters
-    ----------
-    realisation_ids : list[str]
-        List of realisations to generate workflows for. Realisations have the format event:realisation_count, such as Darfield:4.
-    flow_file : Path
-        Path to output flow file (e.g. ~/cylc-src/my-workflow/flow.cylc).
-    goal : list[StageIdentifier]
-        List of workflow outputs to generate.
-    group_goal : list[GroupIdentifier]
-        List of group goals to generate.
-    excluding : list[StageIdentifier]
-        List of stages to exclude.
-    excluding_group : list[GroupIdentifier]
-        List of stage groups to exclude.
-    archive : list[StageIdentifier]
-        Add stage outputs to the archive tarball.
-    visualise : bool
-        Visualise the planned workflow as a graph.
-    show_required_files : bool
-        Print the expected directory tree at the start of the simulation.
-    target_host : WorkflowTarget
-        Select the target host where the workflow will be run.
-    source : Optional[Source]
-        If given, set the source of the realisation. For NSHM and GCMT, the realisation id corresponds to the rupture id and GCMT PublicID respectively.
-    defaults_version : Optional[DefaultsVersion]
-        The simulation defaults to apply for all realisations. Required if source is specified.
-    container : Optional[Path]
-        The container to use for the workflow. If not specified, the default container for the target environment will be used.
-    emod3d_path : Optional[Path]
-        The path to the EMOD3D installation. If not specified, the default path for the target environment will be used.
-    """
-    container = container or CONTAINER_PATHS[target_host]
-    emod3d_path = emod3d_path or EMOD3D_PATHS[target_host]
-    realisations = set.union(
-        *[parse_realisation(realisation_id) for realisation_id in realisation_ids]
-    )
-    if source and not defaults_version:
-        print(
-            "You must specify a defaults version if you specify a source. See the help text for options."
-        )
-        raise typer.Exit(code=1)
-    excluding_set = set(excluding)
-    goal_set = set(goal)
-    if group_goal:
-        goal_set |= set.union(*[GROUP_GOALS[group] for group in group_goal])
-    if excluding_group:
-        excluding_set |= set.union(*[GROUP_STAGES[group] for group in excluding_group])
-
-    excluding_source_map: dict[Optional[Source], set[StageIdentifier]] = {
-        Source.GCMT: {StageIdentifier.GCMTToRealisation},
-        Source.NSHM: {StageIdentifier.NSHMToRealisation},
-    }
-    excluding_set |= set.union(
-        *excluding_source_map.values()
-    ) - excluding_source_map.get(source, set())
-    workflow_plan = create_abstract_workflow_plan(realisations, goal_set, excluding_set)
-    env = jinja2.Environment(
-        loader=jinja2.PackageLoader("workflow"),
-    )
-    archiving = set()
-    for stage_id in archive:
-        archiving |= {
-            file.name for file in stage_outputs(stage_id, include_config_outputs=False)
-        }
-
-    template = env.get_template("flow.cylc")
-    flow_template = template.render(
-        container=container,
-        emod3d_path=emod3d_path,
-        defaults_version=defaults_version,
-        realisations=realisations,
-        target_host=target_host,
-        archiving=archiving,
-        workflow_plan={
-            node: sorted(dependents, key=lambda stage: str(stage))
-            for node, dependents in sorted(
-                nx.to_dict_of_lists(workflow_plan).items(),
-                key=lambda kv: str(kv[0]),
-            )
-        },
-    )
-    flow_file.write_text(
-        # strip empty lines from the output flow template
-        "\n".join(line for line in flow_template.split("\n") if line.strip())
-    )
-    if show_required_files:
-        root_path = Path("cylc-src") / "WORKFLOW_NAME" / "input"
-        inputs = {
-            PurePath(
-                Path("cylc-src") / "WORKFLOW_NAME" / "flow.cylc",
-            )
-        }
-        outputs = set()
-        inputs = set()
-        for stage in workflow_plan.nodes:
-            inputs |= stage.inputs
-            outputs |= stage.outputs
-
-        missing_file_tree = build_filetree(root_path, inputs - outputs)
-
-        if missing_file_tree:
-            print("You require the following files for your simulation:")
-            print()
-            printree.ptree(missing_file_tree)
-            print()
-            print(
-                "You can find documentation for the output files at https://wiki.canterbury.ac.nz/display/QuakeCore/File+Formats+Used+In+Ground+Motion+Simulation."
-            )
-    if visualise:
-        network = pyvis_graph(workflow_plan)
-        with tempfile.NamedTemporaryFile(suffix=".html", delete=False) as graph_render:
-            network.show(graph_render.name, notebook=False)
diff --git a/workflow/templates/flow.cylc b/workflow/templates/flow.cylc
deleted file mode 100644
index cfa9b6c6..00000000
--- a/workflow/templates/flow.cylc
+++ /dev/null
@@ -1,23 +0,0 @@
-{% macro stage_node_identifier(stage) -%}
-{{stage.identifier}}{% if stage.event %}_{{stage.event}}{% if stage.sample %}_{{stage.sample}}{% endif %}{% endif %}
-{%- endmacro -%}
-
-{% macro realisation_identifier(stage) -%}
-{{stage.event}}{% if stage.sample %}_{{stage.sample}}{% endif %}
-{%- endmacro -%}
-
-[scheduling]
-    [[graph]]
-        R1 = """
-        {% for stage, next_stages in workflow_plan.items() -%}
-        {% for next_stage in next_stages %}
-        {{ stage_node_identifier(stage) }} => {{ stage_node_identifier(next_stage) }}
-        {% endfor -%}
-        {% endfor -%}
-        """
-    {% include target_host + '/queue.cylc' %}
-[runtime]
-    {% include target_host + '/root.cylc' %}
-    {% for stage, next_stages in workflow_plan.items() -%}
-    {% include target_host + '/' + stage.identifier + '.cylc' %}
-    {% endfor %}
diff --git a/workflow/templates/hypocentre/archive.cylc b/workflow/templates/hypocentre/archive.cylc
deleted file mode 100644
index 282348c4..00000000
--- a/workflow/templates/hypocentre/archive.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = timestamp=$(date +%Y%m%d%H%M%S) && tar -caf "$timestamp.tar.xz" --files-from=<(find $CYLC_WORKFLOW_SHARE_DIR -type f \( -name "realisation.json" {%- for pattern in archiving %} -o -name "{{pattern}}"  {%- endfor %} \)) && rclone copy "$timestamp.tar.xz" dropbox:/QuakeCoRE/Simulation\ Results\ Inbox/$USER/
diff --git a/workflow/templates/hypocentre/bb_sim.cylc b/workflow/templates/hypocentre/bb_sim.cylc
deleted file mode 100644
index ecf8254f..00000000
--- a/workflow/templates/hypocentre/bb_sim.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share,$CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}:/parent" {{container}} bb-sim /share/realisation.json /stations.vs30 /share/LF/OutBin /share/realisation.hf /parent/Velocity_Model /share/realisation.bb
-        inherit = large_job
diff --git a/workflow/templates/hypocentre/check_domain.cylc b/workflow/templates/hypocentre/check_domain.cylc
deleted file mode 100644
index 1aa04d7e..00000000
--- a/workflow/templates/hypocentre/check_domain.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share,$CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}:/parent" {{container}} check-domain /share/realisation.json /share/realisation.srf /parent/Velocity_Model
diff --git a/workflow/templates/hypocentre/check_srf.cylc b/workflow/templates/hypocentre/check_srf.cylc
deleted file mode 100644
index 9fea5766..00000000
--- a/workflow/templates/hypocentre/check_srf.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} check-srf /share/realisation.json /share/realisation.srf
diff --git a/workflow/templates/hypocentre/copy_domain_parameters.cylc b/workflow/templates/hypocentre/copy_domain_parameters.cylc
deleted file mode 100644
index de0d7d70..00000000
--- a/workflow/templates/hypocentre/copy_domain_parameters.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share,$CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}:/parent"  {{container}} copy-domain-parameters /parent/realisation.json /share/realisation.json
diff --git a/workflow/templates/hypocentre/copy_input.cylc b/workflow/templates/hypocentre/copy_input.cylc
deleted file mode 100644
index d33d2ab4..00000000
--- a/workflow/templates/hypocentre/copy_input.cylc
+++ /dev/null
@@ -1,5 +0,0 @@
-[[copy_input]]
-        script = """
-               mkdir -p {% for realisation in realisations %}$CYLC_WORKFLOW_SHARE_DIR/{{realisation[0]}}{% if realisation[1] %}_{{realisation[1]}}{% endif %} {% endfor %}
-               [[ ! -d $CYLC_WORKFLOW_RUN_DIR/input ]] || cp -rn $CYLC_WORKFLOW_RUN_DIR/input/. $CYLC_WORKFLOW_SHARE_DIR
-        """
diff --git a/workflow/templates/hypocentre/create_e3d_par.cylc b/workflow/templates/hypocentre/create_e3d_par.cylc
deleted file mode 100644
index 90a29675..00000000
--- a/workflow/templates/hypocentre/create_e3d_par.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec --bind "/mnt:/mnt" {{container}} create-e3d-par $CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}/realisation.json $CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}/realisation.srf $CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}/Velocity_Model $CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}/stations $CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}/model $CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}/LF --emod3d-path {{emod3d_path}} --scratch-ffp $CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}/LF
diff --git a/workflow/templates/hypocentre/emod3d.cylc b/workflow/templates/hypocentre/emod3d.cylc
deleted file mode 100644
index 5159f16c..00000000
--- a/workflow/templates/hypocentre/emod3d.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = mpirun --use-hwthread-cpus -n 48 {{emod3d_path}} -args "par=$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}/LF/e3d.par"
-        inherit = large_job
diff --git a/workflow/templates/hypocentre/gcmt_to_realisation.cylc b/workflow/templates/hypocentre/gcmt_to_realisation.cylc
deleted file mode 100644
index 1ea59f29..00000000
--- a/workflow/templates/hypocentre/gcmt_to_realisation.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} gcmt-to-realisation {{stage.event}} {{defaults_version}} /share/realisation.json
diff --git a/workflow/templates/hypocentre/generate_station_coordinates.cylc b/workflow/templates/hypocentre/generate_station_coordinates.cylc
deleted file mode 100644
index 2c3c2ea2..00000000
--- a/workflow/templates/hypocentre/generate_station_coordinates.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-    script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} generate-station-coordinates /share/realisation.json /share/stations --stat-file /stations.ll
diff --git a/workflow/templates/hypocentre/generate_stoch.cylc b/workflow/templates/hypocentre/generate_stoch.cylc
deleted file mode 100644
index 93aedd2c..00000000
--- a/workflow/templates/hypocentre/generate_stoch.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} generate-stoch /share/realisation.json /share/realisation.srf /share/realisation.stoch
diff --git a/workflow/templates/hypocentre/generate_velocity_model.cylc b/workflow/templates/hypocentre/generate_velocity_model.cylc
deleted file mode 100644
index 261d4159..00000000
--- a/workflow/templates/hypocentre/generate_velocity_model.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} sh -c 'generate-velocity-model /share/realisation.json /share/Velocity_Model --num-threads $(nproc) --velocity-model-bin-path /Velocity-Model/NZVM'
-        inherit = large_job
diff --git a/workflow/templates/hypocentre/generate_velocity_model_parameters.cylc b/workflow/templates/hypocentre/generate_velocity_model_parameters.cylc
deleted file mode 100644
index 662608da..00000000
--- a/workflow/templates/hypocentre/generate_velocity_model_parameters.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} generate-velocity-model-parameters /share/realisation.json
diff --git a/workflow/templates/hypocentre/hf_sim.cylc b/workflow/templates/hypocentre/hf_sim.cylc
deleted file mode 100644
index 434a956e..00000000
--- a/workflow/templates/hypocentre/hf_sim.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share,$CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}/stations:/stations" {{container}} hf-sim /share/realisation.json /share/realisation.stoch /stations/stations.ll /share/realisation.hf
-        inherit = large_job
diff --git a/workflow/templates/hypocentre/im_calc.cylc b/workflow/templates/hypocentre/im_calc.cylc
deleted file mode 100644
index c305c7d8..00000000
--- a/workflow/templates/hypocentre/im_calc.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share,/mnt/hypo_scratch/ko_matrices:/ko_matrices" {{container}} im-calc /share/realisation.json /share/realisation.bb /share/intensity_measures.parquet --ko-directory /ko_matrices
-        inherit = large_job
diff --git a/workflow/templates/hypocentre/merge_ts.cylc b/workflow/templates/hypocentre/merge_ts.cylc
deleted file mode 100644
index 284f91d7..00000000
--- a/workflow/templates/hypocentre/merge_ts.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share/{{realisation_identifier(stage)}}" merge-ts /share/LF/OutBin /share/LF/OutBin/output.e3d
diff --git a/workflow/templates/hypocentre/nshm_to_realisation.cylc b/workflow/templates/hypocentre/nshm_to_realisation.cylc
deleted file mode 100644
index 81f730d9..00000000
--- a/workflow/templates/hypocentre/nshm_to_realisation.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} nshm2022-to-realisation /nshmdb.db {{stage.event}} /share/realisation.json {{defaults_version}}
diff --git a/workflow/templates/hypocentre/queue.cylc b/workflow/templates/hypocentre/queue.cylc
deleted file mode 100644
index 2266ef98..00000000
--- a/workflow/templates/hypocentre/queue.cylc
+++ /dev/null
@@ -1,4 +0,0 @@
-        [[queues]]
-                [[[large_job]]]
-                        limit = 1
-                        members = large_job
diff --git a/workflow/templates/hypocentre/realisation_to_srf.cylc b/workflow/templates/hypocentre/realisation_to_srf.cylc
deleted file mode 100644
index 3d0c704b..00000000
--- a/workflow/templates/hypocentre/realisation_to_srf.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} realisation-to-srf /share/realisation.json /share/realisation.srf
diff --git a/workflow/templates/hypocentre/root.cylc b/workflow/templates/hypocentre/root.cylc
deleted file mode 100644
index 265bbcbd..00000000
--- a/workflow/templates/hypocentre/root.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[root]]
-        platform = localhost
-[[large_job]]
diff --git a/workflow/templates/hypocentre/write_model_coordinates.cylc b/workflow/templates/hypocentre/write_model_coordinates.cylc
deleted file mode 100644
index c624bdc1..00000000
--- a/workflow/templates/hypocentre/write_model_coordinates.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} generate-model-coordinates /share/realisation.json /share/model
diff --git a/workflow/templates/nesi/archive.cylc b/workflow/templates/nesi/archive.cylc
deleted file mode 100644
index 69204cab..00000000
--- a/workflow/templates/nesi/archive.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        platform = localhost
-        script = timestamp=$(date +%Y%m%d%H%M%S) && tar -caf "$timestamp.tar.xz" --files-from=<(find $CYLC_WORKFLOW_SHARE_DIR -type f \( -name "realisation.json" {%- for pattern in archiving %} -o -name "{{pattern}}"  {%- endfor %} \)) && rclone copy "$timestamp.tar.xz" dropbox:/QuakeCoRE/Simulation\ Results\ Inbox/$USER/
diff --git a/workflow/templates/nesi/bb_sim.cylc b/workflow/templates/nesi/bb_sim.cylc
deleted file mode 100644
index 2eaa52ba..00000000
--- a/workflow/templates/nesi/bb_sim.cylc
+++ /dev/null
@@ -1,6 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share,$CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}:/parent" {{container}} bb-sim /share/realisation.json /stations.vs30 /share/LF/OutBin /share/realisation.hf /parent/Velocity_Model /share/realisation.bb
-        [[[directives]]]
-                --cpus-per-task = 32
-                --time = 01:00:00
-                --partition = milan
diff --git a/workflow/templates/nesi/check_domain.cylc b/workflow/templates/nesi/check_domain.cylc
deleted file mode 100644
index 1aa04d7e..00000000
--- a/workflow/templates/nesi/check_domain.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share,$CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}:/parent" {{container}} check-domain /share/realisation.json /share/realisation.srf /parent/Velocity_Model
diff --git a/workflow/templates/nesi/check_srf.cylc b/workflow/templates/nesi/check_srf.cylc
deleted file mode 100644
index 9fea5766..00000000
--- a/workflow/templates/nesi/check_srf.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} check-srf /share/realisation.json /share/realisation.srf
diff --git a/workflow/templates/nesi/copy_domain_parameters.cylc b/workflow/templates/nesi/copy_domain_parameters.cylc
deleted file mode 100644
index 411873dd..00000000
--- a/workflow/templates/nesi/copy_domain_parameters.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        platform = localhost
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share,$CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}:/parent" {{container}} copy-domain-parameters /parent/realisation.json /share/realisation.json
diff --git a/workflow/templates/nesi/copy_input.cylc b/workflow/templates/nesi/copy_input.cylc
deleted file mode 100644
index 017ff1c9..00000000
--- a/workflow/templates/nesi/copy_input.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[copy_input]]
-        platform = localhost
-        script = "[[ ! -d $CYLC_WORKFLOW_RUN_DIR/input ]] || cp -rn $CYLC_WORKFLOW_RUN_DIR/input/. $CYLC_WORKFLOW_SHARE_DIR"
diff --git a/workflow/templates/nesi/create_e3d_par.cylc b/workflow/templates/nesi/create_e3d_par.cylc
deleted file mode 100644
index 4bd37962..00000000
--- a/workflow/templates/nesi/create_e3d_par.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        platform = localhost
-        script = apptainer exec {{container}} create-e3d-par $CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}/realisation.json $CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}/realisation.srf $CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}/Velocity_Model $CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}/stations $CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}/model $CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}/LF --emod3d-path /nesi/project/nesi00213/opt/maui/hybrid_sim_tools/emod3d-mpi_v3.0.8 --scratch-ffp $CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}/LF
diff --git a/workflow/templates/nesi/emod3d.cylc b/workflow/templates/nesi/emod3d.cylc
deleted file mode 100644
index 90f7f115..00000000
--- a/workflow/templates/nesi/emod3d.cylc
+++ /dev/null
@@ -1,9 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        pre-script = module load foss/2023a
-        script = srun {{emod3d_path}} -args "par=$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}/LF/e3d.par"
-        [[[directives]]]
-                --partition = milan
-                --ntasks = 160
-                --mem-per-cpu = 2000MB
-                --nodes = 2
-                --time = 06:00:00
diff --git a/workflow/templates/nesi/gcmt_to_realisation.cylc b/workflow/templates/nesi/gcmt_to_realisation.cylc
deleted file mode 100644
index 1ecb56d6..00000000
--- a/workflow/templates/nesi/gcmt_to_realisation.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        platform = localhost
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} gcmt-to-realisation {{stage.event}} {{defaults_version}} /share/realisation.json
diff --git a/workflow/templates/nesi/generate_station_coordinates.cylc b/workflow/templates/nesi/generate_station_coordinates.cylc
deleted file mode 100644
index 393ff70c..00000000
--- a/workflow/templates/nesi/generate_station_coordinates.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-    platform = localhost
-    script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} generate-station-coordinates /share/realisation.json /share/stations --stat-file /stations.ll
diff --git a/workflow/templates/nesi/generate_stoch.cylc b/workflow/templates/nesi/generate_stoch.cylc
deleted file mode 100644
index 93aedd2c..00000000
--- a/workflow/templates/nesi/generate_stoch.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} generate-stoch /share/realisation.json /share/realisation.srf /share/realisation.stoch
diff --git a/workflow/templates/nesi/generate_velocity_model.cylc b/workflow/templates/nesi/generate_velocity_model.cylc
deleted file mode 100644
index 60be0e20..00000000
--- a/workflow/templates/nesi/generate_velocity_model.cylc
+++ /dev/null
@@ -1,6 +0,0 @@
-[[ {{stage_node_identifier(stage)}} ]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} sh -c 'generate-velocity-model /share/realisation.json /share/Velocity_Model --num-threads $(nproc) --velocity-model-bin-path /Velocity-Model/NZVM'
-        [[[directives]]]
-                --cpus-per-task = 32
-                --time = 01:00:00
-                --partition = milan
diff --git a/workflow/templates/nesi/generate_velocity_model_parameters.cylc b/workflow/templates/nesi/generate_velocity_model_parameters.cylc
deleted file mode 100644
index 662608da..00000000
--- a/workflow/templates/nesi/generate_velocity_model_parameters.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} generate-velocity-model-parameters /share/realisation.json
diff --git a/workflow/templates/nesi/hf_sim.cylc b/workflow/templates/nesi/hf_sim.cylc
deleted file mode 100644
index bda2cc29..00000000
--- a/workflow/templates/nesi/hf_sim.cylc
+++ /dev/null
@@ -1,6 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share,$CYLC_WORKFLOW_SHARE_DIR/{{stage.event}}/stations:/stations" {{container}} hf-sim /share/realisation.json /share/realisation.stoch /stations/stations.ll /share/realisation.hf
-        [[[directives]]]
-                --cpus-per-task = 32
-                --time = 01:00:00
-                --partition = milan
diff --git a/workflow/templates/nesi/im_calc.cylc b/workflow/templates/nesi/im_calc.cylc
deleted file mode 100644
index f67582bf..00000000
--- a/workflow/templates/nesi/im_calc.cylc
+++ /dev/null
@@ -1,7 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share,/nesi/project/nesi00213/ko_matrices:/ko_matrices" {{container}} im-calc /share/realisation.json /share/realisation.bb /share/intensity_measures.h5 --num-processes 64 --psa-rotd-maximum-memory-allocation 40 --ko-directory /ko_matrices
-        [[[directives]]]
-                --cpus-per-task = 64
-                --time = 01:00:00
-                --mem = 100G
-                --partition = milan
diff --git a/workflow/templates/nesi/merge_ts.cylc b/workflow/templates/nesi/merge_ts.cylc
deleted file mode 100644
index 284f91d7..00000000
--- a/workflow/templates/nesi/merge_ts.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR:/share/{{realisation_identifier(stage)}}" merge-ts /share/LF/OutBin /share/LF/OutBin/output.e3d
diff --git a/workflow/templates/nesi/nshm_to_realisation.cylc b/workflow/templates/nesi/nshm_to_realisation.cylc
deleted file mode 100644
index 278fa9e4..00000000
--- a/workflow/templates/nesi/nshm_to_realisation.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        platform = localhost
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} nshm2022-to-realisation /nshmdb.db {{stage.event}} /share/realisation.json {{defaults_version}}
diff --git a/workflow/templates/nesi/queue.cylc b/workflow/templates/nesi/queue.cylc
deleted file mode 100644
index e69de29b..00000000
diff --git a/workflow/templates/nesi/realisation_to_srf.cylc b/workflow/templates/nesi/realisation_to_srf.cylc
deleted file mode 100644
index 3d0c704b..00000000
--- a/workflow/templates/nesi/realisation_to_srf.cylc
+++ /dev/null
@@ -1,2 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} realisation-to-srf /share/realisation.json /share/realisation.srf
diff --git a/workflow/templates/nesi/root.cylc b/workflow/templates/nesi/root.cylc
deleted file mode 100644
index 79ee4c35..00000000
--- a/workflow/templates/nesi/root.cylc
+++ /dev/null
@@ -1,7 +0,0 @@
-[[root]]
-        platform = mahuika-slurm
-        pre-script = """
-        module load Apptainer
-        """
-        [[[directives]]]
-                --account = nesi00213
diff --git a/workflow/templates/nesi/write_model_coordinates.cylc b/workflow/templates/nesi/write_model_coordinates.cylc
deleted file mode 100644
index 8ba03376..00000000
--- a/workflow/templates/nesi/write_model_coordinates.cylc
+++ /dev/null
@@ -1,3 +0,0 @@
-[[{{stage_node_identifier(stage)}}]]
-        platform = localhost
-        script = apptainer exec -c --bind "$PWD:/out,$CYLC_WORKFLOW_SHARE_DIR/{{realisation_identifier(stage)}}:/share" {{container}} generate-model-coordinates /share/realisation.json /share/model