Index of modules

A
Align [Biokepi_bfx_tools.Star.Configuration]
All_downloads
Aln [Biokepi_bfx_tools.Bwa.Configuration]
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
Bedtools [Biokepi_bfx_tools]
Biokepi	Top-level entry point into the library
Biokepi_bfx_tools	Catch-all list of parameters to be concatted together and passed to the command.
Biokepi_environment_setup	The default location from where we download opam.
Biokepi_pipeline_edsl	QueL-like Compiler Optimization Framework
Biokepi_run_environment	Module opened by default (like Pervasives) for our library.
Biopam [Biokepi_environment_setup]
Bqsr [Biokepi_bfx_tools.Gatk.Configuration]
Build_machine [Biokepi_environment_setup]
Bwa [Biokepi_bfx_tools]
C
Cat [Biokepi_run_environment.Workflow_utilities]
Command [Biokepi_run_environment.Common.KEDSL]
Common [Biokepi_bfx_tools.Bwa.Configuration]
Common [Biokepi_run_environment]
Common_pipelines [Biokepi_pipeline_edsl]
Compile [Biokepi.EDSL]	Various compilers to “interpret” the EDSL.
Compiler [Biokepi_pipeline_edsl.Pipeline]
Conda [Biokepi_environment_setup]
Configuration [Biokepi_bfx_tools.Virmid]
Configuration [Biokepi_bfx_tools.Stringtie]
Configuration [Biokepi_bfx_tools.Strelka]
Configuration [Biokepi_bfx_tools.Star]
Configuration [Biokepi_bfx_tools.Somaticsniper]
Configuration [Biokepi_bfx_tools.Mutect]
Configuration [Biokepi_bfx_tools.Muse]
Configuration [Biokepi_bfx_tools.Hisat]
Configuration [Biokepi_bfx_tools.Gatk]
Configuration [Biokepi_bfx_tools.Bwa]
Configuration [Biokepi_bfx_tools.Bedtools]
Construct [Biokepi_pipeline_edsl.Pipeline]
Cufflinks [Biokepi_bfx_tools]
Cycledash [Biokepi_bfx_tools]
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]
Download [Biokepi_run_environment.Workflow_utilities]
Download_reference_genomes [Biokepi_environment_setup]
E
EDSL [Biokepi]	The Embedded Bioinformatics Domain Specific Language
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
Gatk [Biokepi_bfx_tools]
Gatk_config [Biokepi_bfx_tools.Gatk.Configuration]
Generic_optimizer [Biokepi_pipeline_edsl.Optimization_framework]	The default, generic optimizer.
Gunzip [Biokepi_run_environment.Workflow_utilities]
H
Hisat [Biokepi_bfx_tools]
I
Indel_realigner [Biokepi_bfx_tools.Gatk.Configuration]
Input [Biokepi_pipeline_edsl.Pipeline_library]
Insane_library [Ttfi_pipeline.Somatic_simplish]
Intersect [Biokepi_bfx_tools.Bedtools.Configuration]
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.
Kallisto [Biokepi_bfx_tools]
Ketrew [Biokepi_run_environment.Common]	and then we forbid any other access to Ketrew, to force everything to throught the above module.
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]
Mark_duplicates_settings [Biokepi_bfx_tools.Picard]
Mem [Biokepi_bfx_tools.Bwa.Configuration]
Metadata [Biokepi]	Values describing the current version of the library.
Metadata [Biokepi_run_environment]
Mosaik [Biokepi_bfx_tools]
Muse [Biokepi_bfx_tools]
Mutect [Biokepi_bfx_tools]
Mutect2 [Biokepi_bfx_tools.Gatk.Configuration]
N
Name [Biokepi_run_environment.Reference_genome.Specification.Default]
O
Optimization_framework [Biokepi_pipeline_edsl]
Optitype [Biokepi_bfx_tools]
P
Picard [Biokepi_bfx_tools]
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]
Print_reads [Biokepi_bfx_tools.Gatk.Configuration]
R
Realigner_target_creator [Biokepi_bfx_tools.Gatk.Configuration]
Ref_genome [All_downloads]
Reference_genome [Biokepi_run_environment]
Region [Biokepi_run_environment]
Remove [Biokepi_bfx_tools.Varscan]
Remove [Biokepi_bfx_tools.Stringtie]
Remove [Biokepi_bfx_tools.Star]
Remove [Biokepi_bfx_tools.Somaticsniper]
Remove [Biokepi_bfx_tools.Samtools]
Remove [Biokepi_bfx_tools.Picard]
Remove [Biokepi_bfx_tools.Mutect]
Remove [Biokepi_bfx_tools.Muse]
Remove [Biokepi_bfx_tools.Mosaik]
Remove [Biokepi_bfx_tools.Hisat]
Remove [Biokepi_bfx_tools.Gatk]
Remove [Biokepi_bfx_tools.Bwa]
Remove [Biokepi_bfx_tools.Bedtools]
Remove [Biokepi_run_environment.Workflow_utilities]
Requirement [Biokepi_run_environment.Machine.Make_fun]
Run_test [Ttfi_pipeline]
S
Samtools [Biokepi_bfx_tools]
Semantics [Biokepi_pipeline_edsl]
Seq2HLA [Biokepi_bfx_tools]
Setup [Biokepi]	Help with the creation of `Biokepi.Machine.t` instances.
Somatic [Biokepi_pipeline_edsl.Common_pipelines]
Somatic_simplish [Ttfi_pipeline]
Somaticsniper [Biokepi_bfx_tools]
Specification [Biokepi_run_environment.Reference_genome]
Star [Biokepi_bfx_tools]
Strelka [Biokepi_bfx_tools]
String [Biokepi_run_environment.Common]	A String module with more capabilities
Stringtie [Biokepi_bfx_tools]
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_def [Biokepi_environment_setup.Tool_providers]
Tool_parameters [Biokepi_run_environment]
Tool_providers [Biokepi_environment_setup]
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
Variant_caller [Biokepi_pipeline_edsl.Pipeline]
Varscan [Biokepi_bfx_tools]
Vcftools [Biokepi_bfx_tools]
Vcftools [Biokepi_run_environment.Workflow_utilities]
Virmid [Biokepi_bfx_tools]
W
Workflow_utilities [Biokepi_run_environment]