Vaccine Design Report
{% for key, val in (patient_summary | default(patient_info)).items() %}
{{ key }}: {{ val }}
{% endfor %}

{% if input_coverage %}{% include "templates/input_coverage.txt" %}{% endif %}
{% include "templates/products.txt" %}
{% if selection_policy is defined %}{% include "templates/selection_policy.txt" %}{% endif %}
{% if ranked_candidates is defined %}{% include "templates/ranking.txt" %}{% endif %}
{% if input_coverage %}{% include "templates/source_outcomes.txt" %}{% endif %}

{% if candidate_details | default(true) and variants %}
{% include "templates/candidate_details.txt" %}
{% endif %}

=== Methods and provenance ===
{% include "templates/source_directory.txt" %}
Prediction evidence
{% for model in prediction_models %}
{{ model.name }} {{ model.version }}: {{ model.status }}
{% endfor %}
Presentation score: the named predictor's presentation output (NetMHCpan: Score_EL).
Presentation score: higher is stronger; presentation percentile: lower is stronger.
Score: Vaxrank's configured per-allele ranking score, shared across predictor rows.
Integrated processing: the named predictor's antigen-processing model, not Pepsickle.
Processing: Pepsickle cleavage annotation; combined is sqrt(C-term * (1 - max internal)).
WT: recorded comparator, not evidence of an observed patient-normal sequence.


{% if input_coverage %}{% include "templates/input_lineage.txt" %}{% endif %}
{% for key, val in patient_info.items() %}{{ key }}: {{ val }}
{% endfor %}
{% if prediction_configuration %}
=== Effective prediction configuration ===
{% for stage in prediction_configuration %}
{{ stage.stage }}: {{ stage.status }}
{% for detail in stage.details %}  {{ detail }}
{% endfor %}
{% endfor %}
{% endif %}

Invocation arguments, including parser defaults
Resolved selection and assembly settings are shown separately.
{% for key, val in args %}
  {{ key }}: {{ val }}
{% endfor %}

Package versions
{% for key, val in package_versions.items() %}
  {{ key }}: {{ val }}
{% endfor %}
