VcfLib: VcfAllelicPrimitives¶

vcfallelicprimitives · 1 contributor · 1 version

usage: vcfallelicprimitives [options] [file]

options:

`-m, --use-mnps`	Retain MNPs as separate events (default: false)
`-t, --tag-parsed FLAG`
	Tag records which are split apart of a complex allele with this flag

Quickstart¶

from janis_bioinformatics.tools.vcflib.vcfallelicprimitives.versions import VcfAllelicPrimitives_1_0_1

wf = WorkflowBuilder("myworkflow")

wf.step(
    "vcfallelicprimitives_step",
    VcfAllelicPrimitives_1_0_1(
        vcf=None,
    )
)
wf.output("out", source=vcfallelicprimitives_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 vcfallelicprimitives:

# user inputs
janis inputs vcfallelicprimitives > inputs.yaml

inputs.yaml

vcf: vcf.vcf.gz

Run vcfallelicprimitives with:

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

Information¶

ID:	`vcfallelicprimitives`
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<VCF>	VCF output

Additional configuration (inputs)¶

name	type	prefix	position	documentation
vcf	Gzipped<VCF>		3
useMnpsFlag	Optional<Boolean>	-m		Retain MNPs as separate events (default: false)
tagParsed	Optional<String>	-t		Tag records which are split apart of a complex allele with this flag
keepInfoFlag	Optional<Boolean>	-k		Maintain site and allele-level annotations when decomposing. Note that in many cases, such as multisample VCFs, these won’t be valid post-decomposition. For biallelic loci in single-sample VCFs, they should be usable with caution.
keepGenoFlag	Optional<Boolean>	-g		Maintain genotype-level annotations when decomposing. Similar caution should be used for this as for –keep-info.
maxLength	Optional<Integer>	-L		Do not manipulate records in which either the ALT or REF is longer than LEN (default: 200).

Workflow Description Language¶

version development

task vcfallelicprimitives {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File vcf
    Boolean? useMnpsFlag
    String? tagParsed
    Boolean? keepInfoFlag
    Boolean? keepGenoFlag
    Int? maxLength
  }
  command <<<
    set -e
    vcfallelicprimitives \
      ~{if select_first([useMnpsFlag, false]) then "-m" else ""} \
      ~{if defined(tagParsed) then ("-t '" + tagParsed + "'") else ""} \
      ~{if (defined(keepInfoFlag) && select_first([keepInfoFlag])) then "-k" else ""} \
      ~{if (defined(keepGenoFlag) && select_first([keepGenoFlag])) then "-g" else ""} \
      ~{if defined(maxLength) then ("-L " + maxLength) else ''} \
      '~{vcf}'
  >>>
  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: VcfAllelicPrimitives'
doc: |-
  usage: vcfallelicprimitives [options] [file]

  options:
     -m, --use-mnps  Retain MNPs as separate events (default: false)
     -t, --tag-parsed FLAG   Tag records which are split apart of a complex allele with this flag

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

inputs:
- id: vcf
  label: vcf
  type: File
  inputBinding:
    position: 3
- id: useMnpsFlag
  label: useMnpsFlag
  doc: 'Retain MNPs as separate events (default: false)'
  type: boolean
  default: false
  inputBinding:
    prefix: -m
- id: tagParsed
  label: tagParsed
  doc: Tag records which are split apart of a complex allele with this flag
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -t
- id: keepInfoFlag
  label: keepInfoFlag
  doc: |-
    Maintain site and allele-level annotations when decomposing. Note that in many cases, such as multisample VCFs, these won't be valid post-decomposition.  For biallelic loci in single-sample VCFs, they should be usable with caution.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -k
- id: keepGenoFlag
  label: keepGenoFlag
  doc: |-
    Maintain genotype-level annotations when decomposing.  Similar caution should be used for this as for --keep-info.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -g
- id: maxLength
  label: maxLength
  doc: |-
    Do not manipulate records in which either the ALT or REF is longer than LEN (default: 200).
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -L

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

baseCommand: vcfallelicprimitives
arguments: []

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