VcfLib: VcfCombine¶

vcfcombine · 1 contributor · 1 version

usage: vcfcombine [vcf file] [vcf file] …

options:

-h –help This text. -r –region REGION A region specifier of the form chrN:x-y to bound the merge

Combines VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files which are combined when records in multiple files match. Alleles must have identical ordering to be combined into one record. If they do not, multiple records will be emitted

Quickstart¶

from janis_bioinformatics.tools.vcflib.vcfcombine.versions import VcfCombine_1_0_1

wf = WorkflowBuilder("myworkflow")

wf.step(
    "vcfcombine_step",
    VcfCombine_1_0_1(
        vcf=None,
    )
)
wf.output("out", source=vcfcombine_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 vcfcombine:

# user inputs
janis inputs vcfcombine > inputs.yaml

inputs.yaml

vcf:
- vcf_0.vcf
- vcf_1.vcf

Run vcfcombine with:

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

Information¶

ID:	`vcfcombine`
URL:	https://github.com/vcflib/vcflib
Versions:	v1.0.1
Container:	shollizeck/vcflib:1.0.1
Authors:	Sebastian Hollizeck
Citations:	None
Created:	2019-10-18
Updated:	2019-10-18

Outputs¶

name	type	documentation
out	stdout<File>	VCF output

Additional configuration (inputs)¶

name	type	prefix	position	documentation
vcf	Array<VCF>		2
region	Optional<String>	-r	1	A region specifier of the form chrN:x-y to bound the merge

Workflow Description Language¶

version development

task vcfcombine {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Array[File] vcf
    String? region
  }
  command <<<
    set -e
    vcfcombine \
      ~{if defined(region) then ("-r '" + region + "'") else ""} \
      ~{if length(vcf) > 0 then "'" + sep("' '", vcf) + "'" else ""}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "shollizeck/vcflib:1.0.1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = stdout()
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'VcfLib: VcfCombine'
doc: |-
  usage: vcfcombine [vcf file] [vcf file] ...

   options:
  -h --help  This text.
  -r --region REGION A region specifier of the form chrN:x-y to bound the merge

  Combines VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files which are combined when records in multiple files match. Alleles must have identical ordering to be combined into one record. If they do not, multiple records will be emitted

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: shollizeck/vcflib:1.0.1

inputs:
- id: vcf
  label: vcf
  type:
    type: array
    items: File
  inputBinding:
    position: 2
- id: region
  label: region
  doc: A region specifier of the form chrN:x-y to bound the merge
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -r
    position: 1

outputs:
- id: out
  label: out
  doc: VCF output
  type: stdout
stdout: _stdout
stderr: _stderr

baseCommand: vcfcombine
arguments: []

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