{% for node in group.nodes %}

{{ node.number }} {% if node.kind == 'step' %}{{ node.item.software|default:"New command" }}{% elif node.kind == 'call' %}{% if node.anchor %}{{ node.item.call|default:"Choose block" }}{% else %}{{ node.item.call|default:"Choose block" }}{% endif %}{% else %}For each sample{% endif %} {{ node.summary }}

{% if node.kind == 'step' %} Software Parameters Run environment {% include "ui3/protocols/_env_combo.html" with name=node.env_input_name empty_label="Default worker environment" by_name=1 selected_name=node.item.env selected_env=node.env_obj %}

Outputs and execution options

Outputs {% include "ui3/protocols/_template_pairs.html" with path=node.paths.outputs rows=node.output_rows add_label="output" %} Optional. Name the file this command writes, then use that name in a later command. Open How later steps use an output above the pipeline for where the name is stored.

Version check Run locally GPU

{% elif node.kind == 'call' %} Block

Arguments {% include "ui3/protocols/_template_pairs.html" with path=node.paths.args rows=node.arg_rows add_label="argument" %} Optional. {% verbatim %}A row bam = {{sample.dedup_bam}} is read inside the block as {{bam}}.{% endverbatim %}

{% else %} {% include "ui3/protocols/_template_items.html" with group=node.children remove_vals="" remove_name="" show_save="" %} {% endif %}

{% endfor %}