10576: Fix formatting in cwl-run-options. Fix dangling refs tutorial-pipeline-workbe...

diff --git a/doc/user/cwl/cwl-run-options.html.textile.liquid b/doc/user/cwl/cwl-run-options.html.textile.liquid
index fea1e51bdf70d70f4496719ccbf14beff16cad1f..c9b18e6df2ef509713061eeb254732db55ef47af 100644 (file)
--- a/doc/user/cwl/cwl-run-options.html.textile.liquid
+++ b/doc/user/cwl/cwl-run-options.html.textile.liquid
@@ -8,29 +8,29 @@ The following command line options are available for @arvados-cwl-runner@:
 
 table(table table-bordered table-condensed).
 |_. Option |_. Description |
-|  --basedir BASEDIR|     Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line).|
-|  --version|             Print version and exit|
-|  --verbose|             Default logging|
-|  --quiet|               Only print warnings and errors.|
-|  --debug|               Print even more logging|
-|  --tool-help|           Print command line help for tool|
-|  --enable-reuse|Enable job reuse (default)|
-|  --disable-reuse|Disable job reuse (always run new jobs).|
-|  --project-uuid UUID|   Project that will own the workflow jobs, if not provided, will go to home project.|
-|  --output-name OUTPUT_NAME|Name to use for collection that stores the final output.|
-|  --output-tags OUTPUT_TAGS|Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.|
-|  --ignore-docker-for-reuse|Ignore Docker image version when deciding whether to reuse past jobs.|
-|  --submit|              Submit workflow to run on Arvados.|
-|  --local|               Control workflow from local host (submits jobs to Arvados).|
-|  --create-template|     (Deprecated) synonym for --create-workflow.|
-|  --create-workflow|     Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See --api.|
-|  --update-workflow UUID|Update an existing Arvados workflow or pipeline template with the given UUID.|
-|  --wait|                After submitting workflow runner job, wait for completion.|
-|  --no-wait|             Submit workflow runner job and exit.|
-|  --api WORK_API|        Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.|
-|  --compute-checksum|    Compute checksum of contents while collecting outputs|
-|  --submit-runner-ram SUBMIT_RUNNER_RAM|RAM (in MiB) required for the workflow runner job (default 1024)|
-|  --name NAME|           Name to use for workflow execution instance.|
+|==--basedir== BASEDIR|     Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line).|
+|==--version==|             Print version and exit|
+|==--verbose==|             Default logging|
+|==--quiet==|               Only print warnings and errors.|
+|==--debug==|               Print even more logging|
+|==--tool-help==|           Print command line help for tool|
+|==--enable-reuse==|Enable job reuse (default)|
+|==--disable-reuse==|Disable job reuse (always run new jobs).|
+|==--project-uuid UUID==|   Project that will own the workflow jobs, if not provided, will go to home project.|
+|==--output-name OUTPUT_NAME==|Name to use for collection that stores the final output.|
+|==--output-tags OUTPUT_TAGS==|Tags for the final output collection separated by commas, e.g., =='--output-tags tag0,tag1,tag2'==.|
+|==--ignore-docker-for-reuse==|Ignore Docker image version when deciding whether to reuse past jobs.|
+|==--submit==|              Submit workflow to run on Arvados.|
+|==--local==|               Control workflow from local host (submits jobs to Arvados).|
+|==--create-template==|     (Deprecated) synonym for ==--create-workflow.==|
+|==--create-workflow==|     Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See ==--api==.|
+|==--update-workflow== UUID|Update an existing Arvados workflow or pipeline template with the given UUID.|
+|==--wait==|                After submitting workflow runner job, wait for completion.|
+|==--no-wait==|             Submit workflow runner job and exit.|
+|==--api== WORK_API|        Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.|
+|==--compute-checksum==|    Compute checksum of contents while collecting outputs|
+|==--submit-runner-ram== SUBMIT_RUNNER_RAM|RAM (in MiB) required for the workflow runner job (default 1024)|
+|==--name== NAME|           Name to use for workflow execution instance.|
 
 h3. Specify workflow and output names
 

diff --git a/doc/user/getting_started/workbench.html.textile.liquid b/doc/user/getting_started/workbench.html.textile.liquid
index a64727fed00fc7df4971da4c12058c65c53ac45c..b397bf4f2ecbed9125b49f2b286d2fa7a6816d40 100644 (file)
--- a/doc/user/getting_started/workbench.html.textile.liquid
+++ b/doc/user/getting_started/workbench.html.textile.liquid
@@ -12,6 +12,6 @@ If you are using the default Arvados instance for this guide, you can Access Arv
 
 You may be asked to log in using a Google account.  Arvados uses only your name and email address from Google services for identification, and will never access any personal information.  If you are accessing Arvados for the first time, the Workbench may indicate your account status is *New / inactive*.  If this is the case, contact the administrator of the Arvados instance to request activation of your account.
 
-Once your account is active, logging in to the Workbench will present you with the Dashboard. This gives a summary of your projects and recent activity in the Arvados instance.  "You are now ready to run your first pipeline.":{{ site.baseurl }}/user/tutorials/tutorial-pipeline-workbench.html
+Once your account is active, logging in to the Workbench will present you with the Dashboard. This gives a summary of your projects and recent activity in the Arvados instance.  "You are now ready to run your first pipeline.":{{ site.baseurl }}/user/tutorials/tutorial-workflow-workbench.html
 
 !{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/workbench-dashboard.png!

diff --git a/doc/user/topics/running-pipeline-command-line.html.textile.liquid b/doc/user/topics/running-pipeline-command-line.html.textile.liquid
index 14c88d1311194b1b576f94209a6dcbf56469d494..c4d3d296af09dcd79df53b7f7dfa536d42a1cee7 100644 (file)
--- a/doc/user/topics/running-pipeline-command-line.html.textile.liquid
+++ b/doc/user/topics/running-pipeline-command-line.html.textile.liquid
@@ -8,7 +8,7 @@ title: "Running an Arvados pipeline"
 If the Jobs API is not available, use the "Common Workflow Language":{{site.baseurl}}/user/cwl/cwl-runner.html instead.
 {% include 'crunch1only_end' %}
 
-This tutorial demonstrates how to use the command line to run the same pipeline as described in "running a pipeline using Workbench.":{{site.baseurl}}/user/tutorials/tutorial-pipeline-workbench.html
+This tutorial demonstrates how to use the command line to run the same pipeline as described in "running a pipeline using Workbench.":{{site.baseurl}}/user/tutorials/tutorial-workflow-workbench.html
 
 {% include 'tutorial_expectations' %}
 {% include 'tutorial_cluster_name' %}

diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index a7682594c9f767bd9cf3d2ef21d466c31004d253..bdd943d393a8ded8e30a542dd00f02fe418ca445 100644 (file)
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -55,7 +55,7 @@ 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:
 

diff --git a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
index d1556cfe028ab881b390d67ab50f05f55499426c..fe80dcb48ebeae24ff20e47cfc2500382d6741b5 100644 (file)
--- a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
@@ -85,6 +85,6 @@ In the editor, enter the following template:
 
 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
 
 For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/methods/pipeline_templates.html