sig
module Configuration :
sig
type t = {
name : string;
vaccine_peptide_length : int;
padding_around_mutation : int;
max_vaccine_peptides_per_mutation : int;
max_mutations_in_report : int;
min_mapping_quality : int;
min_variant_sequence_coverage : int;
min_alt_rna_reads : int;
include_mismatches_after_variant : bool;
use_duplicate_reads : bool;
drop_secondary_alignments : bool;
mhc_epitope_lengths : int list;
reviewers : string list option;
final_reviewer : string option;
xlsx_report : bool;
pdf_report : bool;
ascii_report : bool;
parameters : (string * string) list;
}
val to_json :
Biokepi_bfx_tools.Vaxrank.Configuration.t -> Yojson.Basic.json
val render : Biokepi_bfx_tools.Vaxrank.Configuration.t -> string list
val default : Biokepi_bfx_tools.Vaxrank.Configuration.t
val name : Biokepi_bfx_tools.Vaxrank.Configuration.t -> string
end
type product =
< ascii_report_path : string option;
is_done : Ketrew_pure.Target.Condition.t option;
output_folder_path : string; pdf_report_path : string option;
xlsx_report_path : string option >
val run :
run_with:Biokepi_run_environment.Machine.t ->
configuration:Biokepi_bfx_tools.Vaxrank.Configuration.t ->
reference_build:string ->
vcfs:< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
path : string; .. >
Biokepi_run_environment.Common.KEDSL.workflow_node list ->
bam:Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node ->
predictor:[< `NetMHC
| `NetMHCIIpan
| `NetMHCcons
| `NetMHCcons_IEDB
| `NetMHCpan
| `NetMHCpan_IEDB
| `Random
| `SMM
| `SMM_IEDB
| `SMM_PMBEC
| `SMM_PMBEC_IEDB
> `NetMHC `NetMHCIIpan `NetMHCcons `NetMHCpan ] ->
alleles_file:< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t
option;
path : string; .. >
Biokepi_run_environment.Common.KEDSL.workflow_node ->
output_folder:string ->
< ascii_report_path : string option;
is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
output_folder_path : string; pdf_report_path : string option;
xlsx_report_path : string option >
Biokepi_run_environment.Common.KEDSL.workflow_node
end