Up
Index of types
A
arrow
[
Biokepi_pipeline_edsl.To_dot.Tree
]
B
bam
[
Biokepi_pipeline_edsl.Pipeline
]
bam_file
[
Biokepi_run_environment.Common.KEDSL
]
bam_list
[
Biokepi_run_environment.Common.KEDSL
]
bam_or_bams
[
Biokepi_run_environment.Common.KEDSL
]
bam_pair
[
Biokepi_pipeline_edsl.Pipeline
]
box
[
Biokepi_pipeline_edsl.To_dot.Tree
]
bqsr
[
Biokepi_bfx_tools.Gatk.Configuration
]
broad_jar_location
[
Biokepi_environment_setup.Tool_providers
]
Mutect (and some other tools) are behind some web-login annoying thing: c.f.
F
fastq
[
Biokepi_pipeline_edsl.Pipeline_library.Input
]
fastq
[
Biokepi_pipeline_edsl.Pipeline
]
fastq_data
[
Biokepi_pipeline_edsl.Pipeline_library.Input
]
fastq_gz
[
Biokepi_pipeline_edsl.Pipeline
]
fastq_reads
[
Biokepi_run_environment.Common.KEDSL
]
fastq_sample
[
Biokepi_pipeline_edsl.Pipeline
]
fastq_sample_info
[
Biokepi_pipeline_edsl.Pipeline
]
file_workflow
[
Biokepi_run_environment.Common.KEDSL
]
from
[
Biokepi_pipeline_edsl.Transform_applications.Apply_optimization_framework.Transformation_types
]
from
[
Biokepi_pipeline_edsl.Optimization_framework.Trans_base
]
from_fastqs
[
Biokepi_pipeline_edsl.Common_pipelines.Somatic
]
G
germline
[
Biokepi_pipeline_edsl.Pipeline
]
gtf
[
Biokepi_pipeline_edsl.Pipeline
]
I
indel_realigner
[
Biokepi_bfx_tools.Gatk.Configuration
]
input
[
Biokepi_pipeline_edsl.Pipeline.Variant_caller
]
input_fastq
[
Biokepi_pipeline_edsl.Pipeline.Construct
]
install_target
[
Biokepi_environment_setup.Biopam
]
installable
[
Biokepi_environment_setup.Tool_providers
]
J
json
[
Biokepi_pipeline_edsl.To_json
]
json
[
Biokepi_pipeline_edsl.Pipeline
]
M
metadata_spec
[
Biokepi_pipeline_edsl.Pipeline
]
N
name
[
Biokepi_run_environment.Reference_genome
]
nothing
[
Biokepi_run_environment.Common.KEDSL
]
O
observation
[
Biokepi_pipeline_edsl.To_workflow.Make
]
observation
[
Biokepi_pipeline_edsl.To_json
]
observation
[
Biokepi_pipeline_edsl.To_dot
]
observation
[
Biokepi_pipeline_edsl.To_display
]
observation
[
Biokepi_pipeline_edsl.Semantics.Lambda_calculus
]
observation
[
Biokepi_pipeline_edsl.Optimization_framework.Generic_optimizer
]
optitype_hla_types
[
Biokepi_pipeline_edsl.Pipeline
]
P
phony_workflow
[
Biokepi_run_environment.Common.KEDSL
]
pipeline
[
Biokepi_pipeline_edsl.Pipeline.Compiler
]
pull_function
[
Biokepi_environment_setup.Download_reference_genomes
]
R
repr
[
Biokepi_pipeline_edsl.To_workflow.Make
]
repr
[
Biokepi_pipeline_edsl.To_json
]
repr
[
Biokepi_pipeline_edsl.To_dot
]
repr
[
Biokepi_pipeline_edsl.To_display
]
repr
[
Biokepi_pipeline_edsl.Semantics.Lambda_calculus
]
repr
[
Biokepi_pipeline_edsl.Optimization_framework.Generic_optimizer
]
S
seq2hla_hla_types
[
Biokepi_pipeline_edsl.Pipeline
]
Seq2HLA & Optitype have unique return file formats
somatic
[
Biokepi_pipeline_edsl.Pipeline
]
T
t
[
Biokepi_pipeline_edsl.To_workflow.File_type_specification
]
t
[
Biokepi_pipeline_edsl.To_dot.Tree
]
t
[
Biokepi_pipeline_edsl.Pipeline_library.Input
]
t
[
Biokepi_pipeline_edsl.Pipeline.Compiler
]
t
[
Biokepi_pipeline_edsl.Pipeline.Variant_caller
]
t
[
Biokepi_pipeline_edsl.Pipeline.File
]
t
[
Biokepi_pipeline_edsl.Pipeline
]
t
[
Biokepi_bfx_tools.Virmid.Configuration
]
t
[
Biokepi_bfx_tools.Stringtie.Configuration
]
t
[
Biokepi_bfx_tools.Strelka.Configuration
]
t
[
Biokepi_bfx_tools.Star.Configuration.Align
]
t
[
Biokepi_bfx_tools.Somaticsniper.Configuration
]
t
[
Biokepi_bfx_tools.Picard.Mark_duplicates_settings
]
t
[
Biokepi_bfx_tools.Mutect.Configuration
]
t
[
Biokepi_bfx_tools.Muse.Configuration
]
t
[
Biokepi_bfx_tools.Hisat.Configuration
]
t
[
Biokepi_bfx_tools.Gatk.Configuration.Mutect2
]
t
[
Biokepi_bfx_tools.Gatk.Configuration.Gatk_config
]
t
[
Biokepi_bfx_tools.Bwa.Configuration.Common
]
t
[
Biokepi_bfx_tools.Bedtools.Configuration.Intersect
]
t
[
Biokepi_run_environment.Tool_parameters
]
t
[
Biokepi_run_environment.Region
]
Positions are 1-based
t
[
Biokepi_run_environment.Reference_genome.Specification.Location
]
t
[
Biokepi_run_environment.Reference_genome.Specification
]
t
[
Biokepi_run_environment.Reference_genome
]
A reference genome has a name (for display/matching) and a cluster-dependent path.
t
[
Biokepi_run_environment.Machine.Make_fun.Requirement
]
t
[
Biokepi_run_environment.Machine.Make_fun
]
The type of the “run function” used across the library.
t
[
Biokepi_run_environment.Machine.Tool.Kit
]
t
[
Biokepi_run_environment.Machine.Tool.Definition
]
t
[
Biokepi_run_environment.Machine.Tool
]
t
[
Biokepi_run_environment.Machine
]
term
[
Biokepi_pipeline_edsl.Transform_applications.Apply_optimization_framework.Transformation_types
]
term
[
Biokepi_pipeline_edsl.Optimization_framework.Trans_base
]
tool
[
Biokepi_run_environment.Machine.Tool.Kit
]
tool_type
[
Biokepi_environment_setup.Biopam
]
V
vcf
[
Biokepi_pipeline_edsl.Pipeline
]
W
workflow_option
[
Biokepi_pipeline_edsl.Pipeline.Compiler
]
workflow_option_failure_mode
[
Biokepi_pipeline_edsl.Pipeline.Compiler
]