A normal protocol lists every command. A protocol template is the short form when the same commands run on each sample, such as each replicate. You can also list commands that combine those samples. BioQueue expands the template into a full command list when a job runs.
This page opens an example: a block named process_sample, called once per sample. Replace the echo command with your own software and arguments.
- Name is required. Description is optional.
- Samples. Files per sample starts at 1, which means one input file per sample. Use 2 for paired reads. The name pattern and extra fields are optional.
- Blocks are optional named lists of commands. The pipeline can hold those commands directly instead.
- Pipeline is the run order. A sample map is optional. Use one to repeat commands for every sample, then add commands after it when a step needs every sample.
- Commands. Software is required. Parameters, outputs, environment, version check, local run, and GPU are optional.
{% verbatim %}Inside a sample map, {{sample.r1}} is that sample's first file and {{sample.prefix}} is {{JobName}}_ plus the sample name. After the map, {{samples.prefix}} lists every sample. An output name is stored on the sample when the command runs inside the map ({{sample.clean}}), and as a shared value when the command runs after the map ({{shared.clean}}). A block follows the place it is called.{% endverbatim %}
{{ token_list|json_script:"ui3-tokens" }}
{% include "ui3/protocols/_template_editor.html" %}