def prepare_run_instructions_input_file(tool: Tool, user_inps: dict,
other_inps: dict,
reference_information: str):
yaml_user_inps = CwlTranslator.stringify_translated_inputs(user_inps)
yaml_other_inps = CwlTranslator.stringify_translated_inputs(other_inps)
indented_user = "".join(" " * 7 + s
for s in yaml_user_inps.splitlines(True))
indented_other = "".join(" " * 7 + s
for s in yaml_other_inps.splitlines(True))
not_localising_secondary_warning = ""
if isinstance(tool, WorkflowBase):
inputs_that_arent_localising_secondary_files = [
t.id() for t in tool.tool_inputs()
if t.doc.skip_sourcing_secondary_files
]
if len(inputs_that_arent_localising_secondary_files) > 0:
not_localising_secondary_warning = f"""\
.. warning::
The secondary files for the inputs '{"', '".join(inputs_that_arent_localising_secondary_files)}' will not automatically \
localise using janis prepare and are built just after download. Please note this can take a few hours to build \
before the pipeline runs.
"""
has_static = len(other_inps) > 0
tb = " " * 4
run_args = ["janis run [...run options]", tb + "--inputs inputs.yaml"]
static_generation = ("" if not has_static else f"""\
# static inputs
janis inputs --static {tool.id()} > static.yaml""")
static_yaml = ("" if not has_static else f"""\
**static.yaml**
.. code-block:: yaml
{indented_other}""")
if has_static:
run_args.append(tb + "--inputs static.yaml")
if isinstance(tool, CommandTool) and not tool.container():
run_args.append(
tb +
f"--container-override '{tool.id()}=<organisation/container:version>'"
)
run_args.append(tb + tool.id())
run_statement = " \\\n".join(" " * 3 + el for el in run_args)
if reference_information:
reference_information = f"The following inputs have a suggested source. Using janis prepare with the relevant \
``--source-hint`` will automatically download these files. See `below <#additional-configuration-inputs>`_ for \
more information about inputs for {tool.id()}.\n{reference_information}"
return f"""\
def prepare_run_instructions_input_file(tool: Tool, user_inps: dict,
other_inps: dict,
reference_information: str):
yaml_user_inps = CwlTranslator.stringify_translated_inputs(user_inps)
yaml_other_inps = CwlTranslator.stringify_translated_inputs(other_inps)
indented_user = "".join(" " * 7 + s
for s in yaml_user_inps.splitlines(True))
indented_other = "".join(" " * 7 + s
for s in yaml_other_inps.splitlines(True))
has_static = len(other_inps) > 0
tb = " " * 4
run_args = ["janis run [...run options]", tb + "--inputs inputs.yaml"]
static_generation = ("" if not has_static else f"""\
# static inputs
janis inputs --static {tool.id()} > static.yaml""")
static_yaml = ("" if not has_static else f"""\
**static.yaml**
.. code-block:: yaml
{indented_other}""")
if has_static:
run_args.append(tb + "--inputs static.yaml")
if isinstance(tool, CommandTool) and not tool.container():
run_args.append(
tb +
f"--container-override '{tool.id()}=<organisation/container:version>'"
)
run_args.append(tb + tool.id())
run_statement = " \\\n".join(" " * 3 + el for el in run_args)
return f"""\
