GATK4: LearnReadOrientationModel

Gatk4LearnReadOrientationModel · 1 contributor · 6 versions

TBD

Quickstart

from janis_bioinformatics.tools.gatk4.learnreadorientationmodel.versions import Gatk4LearnReadOrientationModel_4_1_8

wf = WorkflowBuilder("myworkflow")

wf.step(
    "gatk4learnreadorientationmodel_step",
    Gatk4LearnReadOrientationModel_4_1_8(
        f1r2CountsFiles=None,
    )
)
wf.output("out", source=gatk4learnreadorientationmodel_step.out)

OR

1. Install Janis
2. Ensure Janis is configured to work with Docker or Singularity.
3. Ensure all reference files are available:

Note

More information about these inputs are available below.

4. Generate user input files for Gatk4LearnReadOrientationModel:

# user inputs
janis inputs Gatk4LearnReadOrientationModel > inputs.yaml

inputs.yaml

f1r2CountsFiles:
- f1r2CountsFiles_0.tar.gz
- f1r2CountsFiles_1.tar.gz

5. Run Gatk4LearnReadOrientationModel with:

janis run [...run options] \
    --inputs inputs.yaml \
    Gatk4LearnReadOrientationModel

Information

ID:Gatk4LearnReadOrientationModel URL:TBD Versions:4.1.8.1, 4.1.7.0, 4.1.6.0, 4.1.4.0, 4.1.3.0, 4.1.2.0 Container:broadinstitute/gatk:4.1.8.1 Authors:Hollizeck Sebastian Citations:TBD Created:2019-09-09 Updated:2019-09-09

Outputs

name	type	documentation
out	CompressedTarFile	Model file containing information about fragment orientations

Additional configuration (inputs)

name	type	prefix	position	documentation
f1r2CountsFiles	Array<CompressedTarFile>	-I	0	Counts for the read orientation of fragments
javaOptions	Optional<Array<String>>
compression_level	Optional<Integer>			Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2.
numEmIterations	Optional<Integer>	–num-em-iterations	1	Amount of iterations for the em process before it bails
modelFileOut	Optional<Filename>	-O	3

Workflow Description Language

version development

task Gatk4LearnReadOrientationModel {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Array[String]? javaOptions
    Int? compression_level
    Array[File] f1r2CountsFiles
    Int? numEmIterations
    String? modelFileOut
  }
  command <<<
    set -e
    gatk LearnReadOrientationModel \
      --java-options '-Xmx~{((select_first([runtime_memory, 32, 4]) * 3) / 4)}G ~{if (defined(compression_level)) then ("-Dsamjdk.compress_level=" + compression_level) else ""} ~{sep(" ", select_first([javaOptions, []]))}' \
      ~{if length(f1r2CountsFiles) > 0 then "-I '" + sep("' -I '", f1r2CountsFiles) + "'" else ""} \
      ~{if defined(select_first([numEmIterations, 30])) then ("--num-em-iterations " + select_first([numEmIterations, 30])) else ''} \
      -O '~{select_first([modelFileOut, "generated.tar.gz"])}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "broadinstitute/gatk:4.1.8.1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 32, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([modelFileOut, "generated.tar.gz"])
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'GATK4: LearnReadOrientationModel'
doc: TBD

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: broadinstitute/gatk:4.1.8.1

inputs:
- id: javaOptions
  label: javaOptions
  type:
  - type: array
    items: string
  - 'null'
- id: compression_level
  label: compression_level
  doc: |-
    Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2.
  type:
  - int
  - 'null'
- id: f1r2CountsFiles
  label: f1r2CountsFiles
  doc: Counts for the read orientation of fragments
  type:
    type: array
    inputBinding:
      prefix: -I
    items: File
  inputBinding:
    position: 0
- id: numEmIterations
  label: numEmIterations
  doc: Amount of iterations for the em process before it bails
  type: int
  default: 30
  inputBinding:
    prefix: --num-em-iterations
    position: 1
- id: modelFileOut
  label: modelFileOut
  type:
  - string
  - 'null'
  default: generated.tar.gz
  inputBinding:
    prefix: -O
    position: 3

outputs:
- id: out
  label: out
  doc: Model file containing information about fragment orientations
  type: File
  outputBinding:
    glob: generated.tar.gz
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- gatk
- LearnReadOrientationModel
arguments:
- prefix: --java-options
  position: -1
  valueFrom: |-
    $("-Xmx{memory}G {compression} {otherargs}".replace(/\{memory\}/g, (([inputs.runtime_memory, 32, 4].filter(function (inner) { return inner != null })[0] * 3) / 4)).replace(/\{compression\}/g, (inputs.compression_level != null) ? ("-Dsamjdk.compress_level=" + inputs.compression_level) : "").replace(/\{otherargs\}/g, [inputs.javaOptions, []].filter(function (inner) { return inner != null })[0].join(" ")))

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: Gatk4LearnReadOrientationModel