Index of types


A
arrow [Biokepi_pipeline_edsl.To_dot.Tree]

B
bam [Biokepi_pipeline_edsl.Pipeline_library.Input]
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]

E
e [Biokepi_pipeline_edsl.To_dot.Tree.Index_anything]

F
fastq [Biokepi_pipeline_edsl.Pipeline_library.Input]
fastq [Biokepi_pipeline_edsl.Pipeline]
fastq_data [Biokepi_pipeline_edsl.Pipeline_library.Input]
fastq_fragment [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]

H
how [Biokepi_pipeline_edsl.Pipeline_library.Input]

I
input [Biokepi_pipeline_edsl.Pipeline.Variant_caller]
input_fastq [Biokepi_pipeline_edsl.Pipeline.Construct]

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
parameters [Biokepi_pipeline_edsl.To_dot]
phony_workflow [Biokepi_run_environment.Common.KEDSL]
pipeline [Biokepi_pipeline_edsl.Pipeline.Compiler]
predictor_type [Biokepi_run_environment.Hla_utilities]

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]
sorting [Biokepi_pipeline_edsl.Pipeline_library.Input]

T
t [Biokepi_pipeline_edsl.To_workflow.Annotated_file]
t [Biokepi_pipeline_edsl.To_workflow.Provenance_description]
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_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_file_location [Biokepi_run_environment.Workflow_utilities.Download]

V
vcf [Biokepi_pipeline_edsl.Pipeline]
vcf_file [Biokepi_run_environment.Common.KEDSL]

W
workflow_option [Biokepi_pipeline_edsl.Pipeline.Compiler]
workflow_option_failure_mode [Biokepi_pipeline_edsl.Pipeline.Compiler]