Index of modules


A
All_downloads
Annotated_file [Biokepi_pipeline_edsl.To_workflow]
Apply [Biokepi_pipeline_edsl.Transform_applications]
Biokepi_pipeline_edsl.Transform_applications.Apply is the entry point that transforms EDSL terms.
Apply_functions [Biokepi.EDSL.Transform]
Apply as much EDSL functions as possible to their arguments (including list_map).
Apply_optimization_framework [Biokepi_pipeline_edsl.Transform_applications]

B
Biokepi
Top-level entry point into the library
Biokepi_pipeline_edsl
QueL-like Compiler Optimization Framework
Biokepi_run_environment
Module opened by default (like Pervasives) for our library.

C
Cat [Biokepi_run_environment.Workflow_utilities]
Command [Biokepi_run_environment.Common.KEDSL]
Common [Biokepi_run_environment]
Common_pipelines [Biokepi_pipeline_edsl]
Compile [Biokepi.EDSL]
Various compilers to “interpret” the EDSL.
Compiler [Biokepi_pipeline_edsl.Pipeline]
Construct [Biokepi_pipeline_edsl.Pipeline]

D
Default [Biokepi_run_environment.Reference_genome.Specification]
Default [Biokepi_run_environment.Machine.Tool]
Defaults [Biokepi_pipeline_edsl.To_workflow]
Define_transformation [Biokepi_pipeline_edsl.Optimization_framework]
Add the default implementations of the mapping functions
Definition [Biokepi_run_environment.Machine.Tool]
Derive [Biokepi_pipeline_edsl.Pipeline_library.Input]
Download [Biokepi_run_environment.Workflow_utilities]

E
EDSL [Biokepi]
The Embedded Bioinformatics Domain Specific Language
Edsl_input_json

F
File [Biokepi_pipeline_edsl.Pipeline]
File_type_specification [Biokepi_pipeline_edsl.To_workflow]
The link between Biokepi.KEDSL values and EDSL expression types.

G
Generic_optimizer [Biokepi_pipeline_edsl.Optimization_framework]
The default, generic optimizer.
Gunzip [Biokepi_run_environment.Workflow_utilities]

H
Hla_utilities [Biokepi_run_environment]
Hla_utils [Biokepi_pipeline_edsl.To_json]

I
Index_anything [Biokepi_pipeline_edsl.To_dot.Tree]
Input [Biokepi_pipeline_edsl.Pipeline_library]
Insane_library [Ttfi_pipeline.Somatic_simplish]

K
K [Main]
KEDSL [Biokepi]
Bioinformatics-specific extensions to the Ketrew.EDSL module.
KEDSL [Biokepi_run_environment.Common]
This is an experimental extension of Ketrew's EDSL.
Kit [Biokepi_run_environment.Machine.Tool]

L
Language_delta [Biokepi_pipeline_edsl.Transform_applications.Apply_optimization_framework]
Biokepi_pipeline_edsl.Transform_applications.Apply_optimization_framework.Language_delta is where we “intercept” the terms of the language that are interesting.
Library [Biokepi.EDSL]
Library of reusable pieces of pipeline.
Location [Biokepi_run_environment.Reference_genome.Specification]

M
Machine [Biokepi]
The description of the computing infrastructure used in Biokepi.
Machine [Biokepi_run_environment]
Main
Make [Biokepi_pipeline_edsl.To_workflow]
Make [Biokepi_pipeline_edsl.Pipeline_library]
Make_fun [Biokepi_run_environment.Machine]
Jobs in Biokepi ask the computing environment (defined below in Biokepi_run_environment.Machine) for resources.
Make_serializer [Biokepi_pipeline_edsl.To_json]
Metadata [Biokepi]
Values describing the current version of the library.
Metadata [Biokepi_run_environment]

N
Name [Biokepi_run_environment.Reference_genome.Specification.Default]
Name_file [Biokepi_pipeline_edsl.To_workflow]
Name_file [Biokepi_run_environment.Common]
Generate unique filenames for a given set of uniquely identifying properties.

O
Optimization_framework [Biokepi_pipeline_edsl]

P
Pipeline [Biokepi]
Earlier implementation of the Embedded DSL (kept for backwards compatibility).
Pipeline [Biokepi_pipeline_edsl]
Pipeline_insane [Ttfi_pipeline]
Pipeline_library [Biokepi_pipeline_edsl]
Provenance_description [Biokepi_pipeline_edsl.To_workflow]

R
Ref_genome [All_downloads]
Reference_genome [Biokepi_run_environment]
Region [Biokepi_run_environment]
Remove [Biokepi_run_environment.Workflow_utilities]
Requirement [Biokepi_run_environment.Machine.Make_fun]
Run_test [Ttfi_pipeline]

S
Saving_utilities [Biokepi_pipeline_edsl.To_workflow]
Semantics [Biokepi_pipeline_edsl]
Setup [Biokepi]
Help with the creation of Biokepi.Machine.t instances.
Somatic [Biokepi_pipeline_edsl.Common_pipelines]
Somatic_simplish [Ttfi_pipeline]
Specification [Biokepi_run_environment.Reference_genome]
String [Edsl_input_json]
String [Biokepi_pipeline_edsl.To_workflow]
String [Biokepi_run_environment.Common]
A String module with more capabilities

T
Target_tags [Biokepi_run_environment.Common]
An attempt at standardizing “tags.”
The_pass [Biokepi_pipeline_edsl.Transform_applications.Apply]
To_display [Biokepi.EDSL.Compile]
Compiler to SmartPrint.t displayable pseudo code, see the smart-print library.
To_display [Biokepi_pipeline_edsl]
To_dot [Biokepi.EDSL.Compile]
Compiler to DOT graph descriptions.
To_dot [Biokepi_pipeline_edsl]
To_json [Biokepi.EDSL.Compile]
Compiler to JSON (Yojson.Basic.t).
To_json [Biokepi_pipeline_edsl]
To_workflow [Biokepi.EDSL.Compile]
Compiler to Ketrew workflows using the Biokepi.Tools implementations.
To_workflow [Biokepi_pipeline_edsl]
Tool [Biokepi_run_environment.Machine]
Tool_parameters [Biokepi_run_environment]
Tools [Biokepi]
Implementations of the Bioinformatics Ketrew workflow-nodes.
Tools [Biokepi_pipeline_edsl.To_json]
Transform [Biokepi.EDSL]
Transformations on the EDSL.
Transform_applications [Biokepi_pipeline_edsl]
Transformation [Biokepi_pipeline_edsl.Transform_applications.Apply_optimization_framework]
Applying this functor just adds functions that we don't use yet; so this could be simplified in the future.
Transformation_types [Biokepi_pipeline_edsl.Transform_applications.Apply_optimization_framework]
Tree [Biokepi_pipeline_edsl.To_dot]
Ttfi_pipeline
This test uses the high-level EDSL and tries different compilation targets, but does not produce runnable workflows.

U
Unique_id [Biokepi_run_environment.Common]

V
Variable_tool_paths [Biokepi_run_environment.Workflow_utilities]
Variant_caller [Biokepi_pipeline_edsl.Pipeline]
Vcftools [Biokepi_run_environment.Workflow_utilities]

W
Workflow_utilities [Biokepi_run_environment]