[ARVADOS] updated: 7c8e8d37dd25880627a8faabd56eba888ed194b8
git at public.curoverse.com
git at public.curoverse.com
Wed Aug 27 10:38:12 EDT 2014
Summary of changes:
doc/api/schema/PipelineTemplate.html.textile.liquid | 10 +++++++++-
doc/examples/pipeline_templates/gatk-exome-fq-snp.json | 14 +++++++-------
.../tutorials/running-external-program.html.textile.liquid | 1 -
doc/user/tutorials/tutorial-submit-job.html.textile.liquid | 1 -
4 files changed, 16 insertions(+), 10 deletions(-)
via 7c8e8d37dd25880627a8faabd56eba888ed194b8 (commit)
from cf5ffa1f9c3d24fe828cee0993a2e7870719f7e7 (commit)
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commit 7c8e8d37dd25880627a8faabd56eba888ed194b8
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Aug 27 10:38:08 2014 -0400
3342: Update documentation. Add "output_name", remove "output_is_persistent".
diff --git a/doc/api/schema/PipelineTemplate.html.textile.liquid b/doc/api/schema/PipelineTemplate.html.textile.liquid
index 412810f..2b215c2 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 f8c08d1..481dda3 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 at 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 3b9cd16..f13d1c8 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 8be72a2..10abdf0 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"
}
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