+* @"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
+* @"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.
+** @"arvados_sdk_version"@ specifies a version of the Arvados SDK to load alongside the job's script.
+* @"script_parameters"@ describes the component parameters.
+** @"command"@ is the actual command line to invoke the @bwa@ and then @SortSam@. The notation @$()@ denotes macro substitution commands evaluated by the run-command tool wrapper.
+** @"task.stdout"@ indicates that the output of this command should be captured to a file.
+** @$(node.cores)@ evaluates to the number of cores available on the compute node at time the command is run.
+** @$(tmpdir)@ evaluates to the local path for temporary directory the command should use for scratch data.
+** @$(reference_collection)@ evaluates to the script_parameter @"reference_collection"@
+** @$(dir $(...))@ constructs a local path to a directory representing the supplied Arvados collection.
+** @$(file $(...))@ constructs a local path to a given file within the supplied Arvados collection.
+** @$(glob $(...))@ searches the specified path based on a file glob pattern and evalutes to the first result.
+** @$(basename $(...))@ evaluates to the supplied path with leading path portion and trailing filename extensions stripped
+* @"output_of"@ indicates that the @output@ of the @bwa-mem@ component should be used as the @"input"@ script parameter of @SortSam@. Arvados uses these dependencies between components to automatically determine the correct order to run them.