navsection: userguide
title: "Writing a pipeline template"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
{% include 'pipeline_deprecation_notice' %}
* @"name"@ is a human-readable name for the pipeline.
* @"components"@ is a set of scripts or commands that make up the pipeline. Each component is given an identifier (@"bwa-mem"@ and @"SortSam"@) in this example).
-** Each entry in components @"components"@ is an Arvados job submission. For more information about individual jobs, see the "job object reference":{{site.baseurl}}/api/schema/Job.html and "job create method.":{{site.baseurl}}/api/methods/jobs.html#create
+** Each entry in components @"components"@ is an Arvados job submission. For more information about individual jobs, see the "job resource reference.":{{site.baseurl}}/api/methods/jobs.html
* @"repository"@, @"script_version"@, and @"script"@ indicate that we intend to use the external @"run-command"@ tool wrapper that is part of the Arvados. These parameters are described in more detail in "Writing a script":tutorial-firstscript.html.
* @"runtime_constraints"@ describes runtime resource requirements for the component.
** @"docker_image"@ specifies the "Docker":https://www.docker.com/ runtime environment in which to run the job. The Docker image @"bcosc/arv-base-java"@ supplied here has the Java runtime environment, bwa, and samtools installed.
h2. Running your pipeline
-Your new pipeline template should appear at the top of the Workbench "pipeline templates":{{site.arvados_workbench_host}}/pipeline_templates page. You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
+Your new pipeline template should appear at the top of the Workbench "pipeline templates":{{site.arvados_workbench_host}}/pipeline_templates page. You can run your pipeline "using Workbench":tutorial-workflow-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
Test data is available in the "Arvados Tutorial":{{site.arvados_workbench_host}}/projects/qr1hi-j7d0g-u7zg1qdaowykd8d project:
* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":{{site.arvados_workbench_host}}/collections/2463fa9efeb75e099685528b3b9071e0+438 for the "reference_collection" parameter
* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":{{site.arvados_workbench_host}}/collections/3229739b505d2b878b62aed09895a55a+142 for the "sample" parameter
-For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
+For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/methods/pipeline_templates.html
h2. Re-using your pipeline run