Universe=vanilla
executable={{ python }}
error={{ logdir }}/fastq.$(process).out
output={{ logdir }}/fastq.$(process).out
log={{ logdir }}/fastq.log
{% if env %}environment="{{env}}"{% endif %}

{% for arg in args %}
arguments="{{ arg.pyscript }}  {{ arg.sources.0 }} --verbose {% if arg.flowcell %}--flowcell {{ arg.flowcell }}{% endif %} {% if arg.ispaired %}--left {{ arg.target }} --right {{ arg.target_right }}{% else %}--single {{ arg.target }}{% endif %}"
queue
{% endfor %}