Split Multiple Alleles¶

SplitMultiAllele · 2 contributors · 1 version

No documentation was provided: contribute one

Quickstart¶

from janis_bioinformatics.tools.common.splitmultiallele import SplitMultiAllele

wf = WorkflowBuilder("myworkflow")

wf.step(
    "splitmultiallele_step",
    SplitMultiAllele(
        vcf=None,
        reference=None,
    )
)
wf.output("out", source=splitmultiallele_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 SplitMultiAllele:

# user inputs
janis inputs SplitMultiAllele > inputs.yaml

inputs.yaml

reference: reference.fasta
vcf: vcf.vcf

Run SplitMultiAllele with:

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

Information¶

ID:	`SplitMultiAllele`
URL:	No URL to the documentation was provided
Versions:	v0.5772
Container:	heuermh/vt
Authors:	Michael Franklin, Jiaan Yu
Citations:	None
Created:	2019-01-18
Updated:	2020-11-06

Outputs¶

name	type	documentation
out	VCF

Additional configuration (inputs)¶

name	type	prefix	position
vcf	VCF		1
reference	FastaWithIndexes	-r	4
outputFilename	Optional<Filename>	-o	6

Workflow Description Language¶

version development

task SplitMultiAllele {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File vcf
    File reference
    File reference_fai
    File reference_amb
    File reference_ann
    File reference_bwt
    File reference_pac
    File reference_sa
    File reference_dict
    String? outputFilename
  }
  command <<<
    set -e
     \
      vt decompose -s \
      ~{vcf} \
      | vt normalize -n -q - \
      -r ~{reference} \
      -o ~{select_first([outputFilename, "~{basename(vcf, ".vcf")}.norm.vcf"])}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "heuermh/vt"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 8, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "~{basename(vcf, ".vcf")}.norm.vcf"])
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Split Multiple Alleles
doc: ''

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: heuermh/vt

inputs:
- id: vcf
  label: vcf
  type: File
  inputBinding:
    position: 1
    shellQuote: false
- id: reference
  label: reference
  type: File
  secondaryFiles:
  - pattern: .fai
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  - pattern: ^.dict
  inputBinding:
    prefix: -r
    position: 4
    shellQuote: false
- id: outputFilename
  label: outputFilename
  type:
  - string
  - 'null'
  default: generated.norm.vcf
  inputBinding:
    prefix: -o
    position: 6
    valueFrom: $(inputs.vcf.basename.replace(/.vcf$/, "")).norm.vcf
    shellQuote: false

outputs:
- id: out
  label: out
  type: File
  outputBinding:
    glob: $(inputs.vcf.basename.replace(/.vcf$/, "")).norm.vcf
    loadContents: false
stdout: _stdout
stderr: _stderr
arguments:
- position: 0
  valueFrom: 'vt decompose -s '
  shellQuote: false
- position: 2
  valueFrom: '| vt normalize -n -q - '
  shellQuote: false

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