Template editor

{% if editor.mode == 'json' %} {% else %} {% endif %}

Template JSON {% if editor.mode == 'json' %} {% endif %}

Expanded preview {% if editor.preview %}{{ editor.preview|length }} step{{ editor.preview|length|pluralize }} for {{ editor.preview_samples }} sample{{ editor.preview_samples|pluralize }}{% elif editor.preview_error %}Preview needs a correction{% else %}No steps yet{% endif %}

Preview sample count Updates this preview only. The job uses however many samples its input files make. {% if editor.preview_error %}

{% endif %} {% if editor.outline %}

{{ line.text }}

{% endif %} {% if editor.preview %}

{% for st in editor.preview %} {% endfor %}

#	Software	Run environment	Parameter
{{ st.step_order }}	{{ st.software }}	{{ st.env_name\|default:"Default worker environment" }}	{{ st.parameter }}

{% endif %}

{% if editor.mode != 'json' %}

Sample grouping and fieldsHow inputs become samples

Files per sample groups the job's input files. Each sample already has index, name, prefix, r1, r2, and files.

Files per sample Starts at 1: each input file is its own sample. 2 means file 1 and file 2 are sample 1 (paired reads). The number of input files must divide evenly by this value. Default sample name Optional. {% verbatim %}rep{{index}} becomes rep1, rep2, and so on. index starts at 1. A sample sheet on the job can override the name.{% endverbatim %}

Sample fields {% include "ui3/protocols/_template_pairs.html" with path=editor.sample_fields_path rows=editor.sample_field_rows add_label="field" %} Optional. Extra values that can differ per sample. {% verbatim %}A row umi_len = {{UMI_LEN||6}} uses a job parameter, with 6 as the default. Leave this empty when samples only need their files.{% endverbatim %}

How later steps use an output Names for files a command writes

{% verbatim %}

An output row names a file the command writes. The value is that path, for example {{sample.prefix}}.fq.gz. BioQueue does not scan the results folder for new files. A later command uses the name instead of typing the path again.

Each sample already has index, name, prefix, r1, r2, and files. An output adds another name on top of those.

Inside a sample map, or in a block called from that map, the name is stored on the sample that is running.

The next command for that same sample uses {{sample.clean}}.
A command after the map uses {{samples.clean}} for every sample, separated by spaces.
{{samples.first.clean}} is the first sample, {{samples.last.clean}} is the last, and {{samples.2.clean}} is sample 2.

After the map, or in a block called from there, the name is shared by the whole job. A later command uses {{shared.merged_bam}}.

Example. Inside the map, a trim command writes {{sample.prefix}}.fq.gz and records the output name clean. The align command for that sample reads {{sample.clean}}. After every sample is done, a merge command reads {{samples.clean}} and records merged_bam. The report command reads {{shared.merged_bam}}.

A block argument is not an output. On the call, a row bam = {{sample.dedup_bam}} is read inside the block as {{bam}}. The value is filled in at the call, before the block starts.

Saving rejects a placeholder that is one edit away from a name you already declared, such as {{sample.clen}} when the output is clean. A new name such as {{sample.condition}} is kept, and the job asks for it under Samples.

{% endverbatim %}

Pipeline

Entries run from top to bottom. A command runs once. A sample map is optional and runs its entries once per sample. Commands after a map see every sample. {% verbatim %}Inside the map use {{sample.r1}} and {{sample.prefix}}. After the map use {{samples.field}}.{% endverbatim %}

{% include "ui3/protocols/_template_items.html" with group=editor.pipeline remove_vals="" remove_name="" show_save=1 %}

Reusable blocks

Optional. A named list of commands the pipeline can call. Each command needs a software name. Rename a block here; calls to that name are updated with it.

{% for block in editor.blocks %}

{{ block.name }}Reusable block

{% include "ui3/protocols/_template_items.html" with group=block.body remove_vals="" remove_name="" show_save="" %}

{% empty %}

No reusable blocks yet.

{% endfor %}

{% endif %}