X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/76e8998d9326da7d99bcf083bd7234d62c2af63c..e1fd558686c78d6edfd460b7531ec9b559299889:/doc/user/tutorials/running-external-program.html.textile.liquid

diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index 90dc1970a7..bdd943d393 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -4,6 +4,8 @@ navsection: userguide
 title: "Writing a pipeline template"
 ...
 
+{% include 'pipeline_deprecation_notice' %}
+
 This tutorial demonstrates how to construct a two stage pipeline template that uses the "bwa mem":http://bio-bwa.sourceforge.net/ tool to produce a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file, then uses the "Picard SortSam tool":http://picard.sourceforge.net/command-line-overview.shtml#SortSam to produce a BAM (Binary Alignment/Map) file.
 
 {% include 'tutorial_expectations' %}
@@ -20,7 +22,7 @@ This will open the template record in an interactive text editor (as specified b
 
 * @"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.
@@ -53,18 +55,18 @@ See the "run-command reference":{{site.baseurl}}/user/topics/run-command.html fo
 
 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
 
-Arvados allows users to re-use jobs that have the same inputs in order to save computing time and resources. Users are able to change a job downstream without re-computing earlier jobs. This section shows which version control parameters should be tuned to make sure Arvados will not re-compute your jobs. 
+Arvados allows users to re-use jobs that have the same inputs in order to save computing time and resources. Users are able to change a job downstream without re-computing earlier jobs. This section shows which version control parameters should be tuned to make sure Arvados will not re-compute your jobs.
 
 Note: Job reuse can only happen if all input collections do not change.