From 7c8e8d37dd25880627a8faabd56eba888ed194b8 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 27 Aug 2014 10:38:08 -0400 Subject: [PATCH] 3342: Update documentation. Add "output_name", remove "output_is_persistent". --- .../schema/PipelineTemplate.html.textile.liquid | 10 +++++++++- .../pipeline_templates/gatk-exome-fq-snp.json | 14 +++++++------- .../running-external-program.html.textile.liquid | 1 - .../tutorial-submit-job.html.textile.liquid | 1 - 4 files changed, 16 insertions(+), 10 deletions(-) diff --git a/doc/api/schema/PipelineTemplate.html.textile.liquid b/doc/api/schema/PipelineTemplate.html.textile.liquid index 412810f02e..2b215c2ba3 100644 --- a/doc/api/schema/PipelineTemplate.html.textile.liquid +++ b/doc/api/schema/PipelineTemplate.html.textile.liquid @@ -5,13 +5,21 @@ navmenu: Schema title: PipelineTemplate ... -Pipelines consist of a set of "components". Each component is an Arvados job submission. "Parameters for job submissions are described on the job method page.":{{site.baseurl}}/api/methods/jobs.html#create +The pipeline template consists of "name" and "components". table(table table-bordered table-condensed). |_. Attribute |_. Type |_. Accepted values |_. Required|_. Description| |name |string |any |yes |The human-readable name of the pipeline template.| |components |object |JSON object containing job submission objects|yes |The component jobs that make up the pipeline, with the component name as the key. | +h3. Components + +The components field of the pipeline template is a JSON object which describes the individual steps that make up the pipeline. Each component is an Arvados job submission. "Parameters for job submissions are described on the job method page.":{{site.baseurl}}/api/methods/jobs.html#create In addition, a component can have the following parameters: + +table(table table-bordered table-condensed). +|_. Attribute |_. Type |_. Accepted values |_. Required|_. Description| +|output_name |string or boolean|string or false |no |If a string is provided, use this name for the output collection of this component. If the value is false, do not create a permanent output collection (an temporary intermediate collection will still be created). If not provided, a default name will be assigned to the output.| + h3. Script parameters When used in a pipeline, each parameter in the 'script_parameters' attribute of a component job can specify that the input parameter must be supplied by the user, or the input parameter should be linked to the output of another component. To do this, the value of the parameter should be JSON object containing one of the following attributes: diff --git a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json index f8c08d146a..481dda38ca 100644 --- a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json +++ b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json @@ -13,7 +13,7 @@ ], "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi" }, - "output_is_persistent":false + "output_name":false }, "bwa-index":{ "repository":"arvados", @@ -28,7 +28,7 @@ "required":true } }, - "output_is_persistent":false + "output_name":false }, "bwa-aln":{ "repository":"arvados", @@ -54,7 +54,7 @@ "runtime_constraints":{ "max_tasks_per_node":1 }, - "output_is_persistent":false + "output_name":false }, "picard-gatk2-prep":{ "repository":"arvados", @@ -75,7 +75,7 @@ "runtime_constraints":{ "max_tasks_per_node":1 }, - "output_is_persistent":false + "output_name":false }, "GATK2-realign":{ "repository":"arvados", @@ -107,7 +107,7 @@ "runtime_constraints":{ "max_tasks_per_node":2 }, - "output_is_persistent":false + "output_name":false }, "GATK2-bqsr":{ "repository":"arvados", @@ -130,7 +130,7 @@ "required":true } }, - "output_is_persistent":false + "output_name":false }, "GATK2-merge-call":{ "repository":"arvados", @@ -169,7 +169,7 @@ ] } }, - "output_is_persistent":true + "output_name":"Variant calls from UnifiedGenotyper" } } } diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid index 3b9cd165f2..f13d1c8319 100644 --- a/doc/user/tutorials/running-external-program.html.textile.liquid +++ b/doc/user/tutorials/running-external-program.html.textile.liquid @@ -24,7 +24,6 @@ This will open the template record in an interactive text editor (as specified b * @"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 -* @"output_is_persistent"@ indicates whether the output of the component is considered valuable. If this value is false (or not given), the output will be treated as intermediate data which may be eventually deleted to reclaim disk space. * @"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 @"arvados/jobs-java-bwa-samtools"@ supplied here has the Arvados SDK, Java runtime environment, bwa, and samtools installed. * @"script_parameters"@ describes the component parameters. diff --git a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid index 8be72a2365..10abdf0b1c 100644 --- a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid +++ b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid @@ -108,7 +108,6 @@ Next, create a file that contains the pipeline definition: }, "repository":"$USER", "script_version":"master", - "output_is_persistent":true, "runtime_constraints":{ "docker_image":"arvados/jobs-java-bwa-samtools" } -- 2.30.2