Module Biokepi_bfx_tools.Kallisto (.ml)

module Kallisto: sig .. end

Workflow-nodes to run kallisto.

val index : reference_build:string ->
       run_with:Biokepi_run_environment.Machine.t ->
       < exists : Ketrew_pure.Target.Condition.t;
         host : Biokepi_run_environment.Common.KEDSL.Host.t;
         is_bigger_than : int -> Ketrew_pure.Target.Condition.t;
         is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string >
       Biokepi_run_environment.Common.KEDSL.workflow_node

Create a kallisto specific index of the transcriptome (cDNA)

val run : reference_build:string ->
       ?bootstrap_samples:int ->
       run_with:Biokepi_run_environment.Machine.t ->
       fastq:< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
               paths : string * string option; .. >
             Biokepi_run_environment.Common.KEDSL.workflow_node ->
       result_prefix:string ->
       < exists : Ketrew_pure.Target.Condition.t;
         host : Biokepi_run_environment.Common.KEDSL.Host.t;
         is_bigger_than : int -> Ketrew_pure.Target.Condition.t;
         is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string >
       Biokepi_run_environment.Common.KEDSL.workflow_node

Quantify transcript abundance from RNA fastqs, results in abundance.tsv file