Extract Strelka Somatic AD DP

extractStrelkaSomaticADDP · 1 contributor · 2 versions

• Extract and calculate AD and AF value for each variant (both SNVs and INDELs)

Based on https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#somatic

Quickstart

from janis_bioinformatics.tools.pmac.extractstrelkasomaticaddp.versions import ExtractStrelkaSomaticADDP_0_1_1

wf = WorkflowBuilder("myworkflow")

wf.step(
    "extractstrelkasomaticaddp_step",
    ExtractStrelkaSomaticADDP_0_1_1(
        vcf=None,
    )
)
wf.output("out", source=extractstrelkasomaticaddp_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 extractStrelkaSomaticADDP:

# user inputs
janis inputs extractStrelkaSomaticADDP > inputs.yaml

inputs.yaml

vcf: vcf.vcf

5. Run extractStrelkaSomaticADDP with:

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

Information

ID:extractStrelkaSomaticADDP URL:https://github.com/PMCC-BioinformaticsCore/scripts/tree/master/vcf_utils Versions:0.1.1, 0.1.0 Container:michaelfranklin/pmacutil:0.1.1 Authors:Jiaan Yu Citations:None Created:2020-07-27 00:00:00 Updated:2020-07-27 00:00:00

Outputs

name	type	documentation
out	VCF

Additional configuration (inputs)

name	type	prefix	position	documentation
vcf	VCF	-i		input vcf
outputFilename	Optional<Filename>	-o		output vcf

Workflow Description Language

version development

task extractStrelkaSomaticADDP {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File vcf
    String? outputFilename
  }
  command <<<
    set -e
    extract_strelka_somatic_DP_AF.py \
      -i '~{vcf}' \
      -o '~{select_first([outputFilename, "generated.vcf"])}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "michaelfranklin/pmacutil:0.1.1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 8, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "generated.vcf"])
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Extract Strelka Somatic AD DP
doc: |2-

   - Extract and calculate AD and AF value for each variant (both SNVs and INDELs)
  Based on https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#somatic


requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: michaelfranklin/pmacutil:0.1.1

inputs:
- id: vcf
  label: vcf
  doc: input vcf
  type: File
  inputBinding:
    prefix: -i
- id: outputFilename
  label: outputFilename
  doc: output vcf
  type:
  - string
  - 'null'
  default: generated.vcf
  inputBinding:
    prefix: -o

outputs:
- id: out
  label: out
  type: File
  outputBinding:
    glob: generated.vcf
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand: extract_strelka_somatic_DP_AF.py
arguments: []

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