Call Somatic Variants from freebayes¶

callSomaticFreeBayes · 1 contributor · 1 version

Usage: callSomaticFreeBayes.R [options]

Quickstart¶

from janis_bioinformatics.tools.dawson.callsomaticfreebayes.latest import CallSomaticFreeBayesLatest

wf = WorkflowBuilder("myworkflow")

wf.step(
    "callsomaticfreebayes_step",
    CallSomaticFreeBayesLatest(
        vcf=None,
    )
)
wf.output("out", source=callsomaticfreebayes_step.out)

OR

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

Note

More information about these inputs are available below.

Generate user input files for callSomaticFreeBayes:

# user inputs
janis inputs callSomaticFreeBayes > inputs.yaml

inputs.yaml

vcf: vcf.vcf

Run callSomaticFreeBayes with:

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

Information¶

ID:	`callSomaticFreeBayes`
URL:	No URL to the documentation was provided
Versions:	0.1.8
Container:	shollizeck/dawsontoolkit:0.1.8.1
Authors:	Sebastian Hollizeck
Citations:	None
Created:	2019-10-19
Updated:	2019-10-25

Outputs¶

name	type	documentation
out	VCF	To determine type

Additional configuration (inputs)¶

name	type	prefix	documentation
vcf	VCF	-i	input vcf
normalSampleName	Optional<String>	-n	the normal sample name in the vcf (default: first sample in vcf)
outputFilename	Optional<Filename>	-o	output file name (default: STDOUT)

Workflow Description Language¶

version development

task callSomaticFreeBayes {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File vcf
    String? normalSampleName
    String? outputFilename
  }
  command <<<
    set -e
    callSomaticFreeBayes.R \
      -i '~{vcf}' \
      ~{if defined(normalSampleName) then ("-n '" + normalSampleName + "'") else ""} \
      -o '~{select_first([outputFilename, "generated.vcf"])}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 4, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "shollizeck/dawsontoolkit:0.1.8.1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 12, 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: Call Somatic Variants from freebayes
doc: "Usage: callSomaticFreeBayes.R [options]\n"

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: shollizeck/dawsontoolkit:0.1.8.1

inputs:
- id: vcf
  label: vcf
  doc: input vcf
  type: File
  inputBinding:
    prefix: -i
- id: normalSampleName
  label: normalSampleName
  doc: 'the normal sample name in the vcf (default: first sample in vcf)'
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -n
- id: outputFilename
  label: outputFilename
  doc: 'output file name (default: STDOUT)'
  type:
  - string
  - 'null'
  default: generated.vcf
  inputBinding:
    prefix: -o

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

baseCommand: callSomaticFreeBayes.R
arguments: []

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