Merge branch 'main' into upgrade-python-20230920

dbmi-bgm · Sep 28, 2023 · 8381459 · 8381459
2 parents 2c27f66 + 411244c
commit 8381459
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Showing 4 changed files with 46 additions and 2 deletions.
diff --git a/docs/yaml_metaworkflow.rst b/docs/yaml_metaworkflow.rst
@@ -62,6 +62,12 @@ Template
         dependencies:
           - <workflow_name>[@<tag>]
 
+        ## Fixed shards ####################
+        #   Allows to force a fixed shards structure ignoring
+        #     the input structure, scatter and gather dimensions
+        ####################################
+        shards: [[<string>], ..]               # e.g., [['0'], ['1'], ['2']]
+
         ## Lock version ####################
         #   Specific version to use
         #     for the workflow
@@ -96,6 +102,7 @@ Template
             gather: <integer>
             input_dimension: <integer>
             extra_dimension: <integer>
+            gather_input: <integer>
             # All the following fields are optional and provided as example,
             #   can be expanded to anything accepted by the schema
             mount: <boolean>
@@ -188,6 +195,12 @@ dependencies
 Workflows that must complete before kicking the current step.
 List of workflows in the the format ``<workflow_name>[@<tag>]``.
 
+shards
+^^^^^^
+Allows to force a fixed shards structure for the current step.
+Override input structure, scatter and gather dimensions.
+Shards structure as list, e.g., ``[['0'], ['1'], ['2']]``.
+
 version
 ^^^^^^^
 Version to use for the corresponding workflow instead of the default specified for the repository.
@@ -305,3 +318,8 @@ extra_dimension
 Additional increment to dimension used when creating the specific input for the step.
 This will be applied on top of ``gather``, if any, and will only affect the input.
 This will not affect gather dimension in building the pipeline structure.
+
+gather_input
+------------
+Equivalent to ``gather`` in collecting output from previous shards.
+This will not affect scatter or gather dimensions in building pipeline structure.
diff --git a/docs/yaml_workflow.rst b/docs/yaml_workflow.rst
@@ -175,10 +175,25 @@ We recommend to use this new type to implement QCs.
 When using ``quality_metric_generic`` as a ``qc_type``, it is possible to generate two different types of output: a key-value pairs JSON file and a compressed file.
 The JSON file can be used to create a summary report of the quality metrics generated by the QC process.
 The compressed file can be used to store the original output for the QC, including additional data or graphs.
-Both the JSON file and compressed file will be attached to the file specified as target by ``argument_to_be_attached_to``.
-The content of the JSON file will be patched directly on the target file, while the compressed file will be made available for download on the file via a link.
+Both the JSON file and compressed file will be attached to the file specified as target by ``argument_to_be_attached_to`` with a ``QualityMetricGeneric`` object.
+The content of the JSON file will be patched directly on the object, while the compressed file will be made available for download via a link.
 The output type can be specified by setting ``json: True`` or ``zipped: True`` in the the QC output definition.
 
+Template for ``quality_metric_generic``:
+
+.. code-block:: python
+
+  }
+    "name": "Quality metric name",
+    "qc_values": [
+      {
+        "key": "Name of the key",
+        "tooltip": "Tooltip for the key",
+        "value": "Value for the key"
+      }
+    ]
+  }
+
 secondary_files
 ^^^^^^^^^^^^^^^
 This field can be used for output **files**.

diff --git a/pipeline_utils/lib/yaml_parser.py b/pipeline_utils/lib/yaml_parser.py
@@ -359,6 +359,7 @@ class YAMLMetaWorkflow(YAMLTemplate):
     OUTPUT_SCHEMA = 'output'
     CONFIG_SCHEMA = 'config'
     DEPENDENCIES_SCHEMA = 'dependencies'
+    SHARDS_SCHEMA = 'shards'
     PROBAND_ONLY_SCHEMA = 'proband_only'
 
     def __init__(self, data):
@@ -446,6 +447,9 @@ def _workflows(self, version, project):
             # hard dependencies
             if values.get(self.DEPENDENCIES_SCHEMA):
                 workflow_[self.DEPENDENCIES_SCHEMA] = values[self.DEPENDENCIES_SCHEMA]
+            # fixed shards
+            if values.get(self.SHARDS_SCHEMA):
+                workflow_[self.SHARDS_SCHEMA] = values[self.SHARDS_SCHEMA]
             workflows.append(workflow_)
 
         return workflows

diff --git a/pipeline_utils/schemas/yaml_metaworkflow.py b/pipeline_utils/schemas/yaml_metaworkflow.py
@@ -65,6 +65,10 @@
                             schema.ITEMS: {
                                 schema.TYPE: schema.STRING
                             }
+                        },
+                        'shards': {
+                            schema.DESCRIPTION: 'Shards structure to create for the step',
+                            schema.TYPE: schema.ARRAY
                         }
                     },
                     schema.REQUIRED: ['input', 'config']
@@ -107,6 +111,9 @@
                 'gather': {
                     schema.TYPE: schema.NUMBER
                 },
+                'gather_input': {
+                    schema.TYPE: schema.NUMBER
+                },
                 'input_dimension': {
                     schema.TYPE: schema.NUMBER
                 },