Jinja templates

These templates are filled with the Input dictionary and the Input environment variables that are generated by the workflow for each task.

The job.sh template

This template is used by woom.tasks.Task.render_content() to create the job script.

Default job.sh jinja template

{% block header -%}
#!/bin/bash

# Prolog
set -eo pipefail
on_exit() {
    status=$?
    echo $status > "$WOOM_SUBMISSION_DIR/job.status"
    exit $status
}
trap on_exit EXIT
{% endblock %}

{% block env -%}
{{ task.export_env(params) }}
{% endblock %}

{% block pre_run -%}
# Go to run dir
{{ task.export_run_dir() }}
{% endblock %}

{% block run -%}
# Run the commandline(s)
{{ task.export_commandline() }}
{% endblock %}

{% block post_run -%}
{% if task.artifacts %}
# Check artifacts
{{ task.export_artifacts_checking() }}
{% endif %}
{% endblock %}

The env.sh template

This template is used by woom.env.EnvConfig.render() to format the environment declaration in The job.sh template.

Default env.sh jinja template

{% block raw_text -%}
{% if env.raw_text %}
# Raw init env
{{ env.raw_text }}
{% endif %}
{% endblock %}
{% block modules -%}
{% if env.module_load %}

# Environment modules
{% if env.module_setup %}
{{ env.module_setup }}
{% endif %}
{% if env.module_use %}
module use {{ env.module_use }}
{% endif %}
{% if env.module_load %}
module load {{ env.module_load }}
{% endif %}
{% endif %}
{% endblock %}
{% block uv -%}
{% if workflow_dir is defined %}
{% set venv_activate = os.path.join(workflow_dir, ".venv", "bin", "activate") %}
{% if env.uv_venv is true or (env.uv_env is none and os.path.exists(venv_activate)) %}

# UV virtual environment
source {{ venv_activate }}
{% endif %}
{% endif %}
{% endblock %}
{% block env_vars -%}
{% if env.has_vars() %}
# Environment variables
{# forward #}
{% for name in env.vars_forward %}
export {{ name }}="{{ os.environ[name] }}"
{% endfor %}
{# set #}
{% for name, value in env.vars_set.items() %}
export {{ name }}="{{ value|as_str_env }}"
{% endfor %}
{# prepend #}
{% for name, value in env.vars_prepend.items() %}
export {{ name }}={{ value|as_str_env }}{{ os.pathsep }}${{ name }}
{% endfor %}
{# append #}
{% for name, value in env.vars_append.items() %}
export {{ name }}=${{ name }}{{ os.pathsep }}{{ value|as_str_env }}
{% endfor %}
{% endif %}
{% endblock %}
{% block conda -%}
{% if env.conda_activate %}

# Conda
{% if env.conda_setup %}
{{ env.conda_setup }}
{% endif %}
conda activate {{ env.conda_activate }}
{% endif %}
{% endblock %}

{% block custom -%}
{# Custom configuration block #}
{% endblock %}