Filter Vardict Somatic Vcf¶

FilterVardictSomaticVcf · 2 contributors · 1 version

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Quickstart¶

from janis_bioinformatics.tools.common.filtervardictsomaticvcf import FilterVardictSomaticVcf

wf = WorkflowBuilder("myworkflow")

wf.step(
    "filtervardictsomaticvcf_step",
    FilterVardictSomaticVcf(

    )
)
wf.output("out", source=filtervardictsomaticvcf_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 FilterVardictSomaticVcf:

# user inputs
janis inputs FilterVardictSomaticVcf > inputs.yaml

inputs.yaml

{}

Run FilterVardictSomaticVcf with:

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

Information¶

ID:	`FilterVardictSomaticVcf`
URL:	No URL to the documentation was provided
Versions:	v1.9
Container:	biocontainers/bcftools:v1.9-1-deb_cv1
Authors:	Jiaan Yu, Michael Franklin
Citations:	None
Created:	2020-06-04
Updated:	2020-11-09

Outputs¶

name	type	documentation
out	VCF

Additional configuration (inputs)¶

name	type	prefix	position	documentation
vcf	Optional<VCF>		1
outputFilename	Optional<Filename>	-o	3

Workflow Description Language¶

version development

task FilterVardictSomaticVcf {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File? vcf
    String? outputFilename
  }
  command <<<
    set -e
     \
      bcftools filter -e 'STATUS="GERMLINE"' -o - \
      ~{if defined(vcf) then ("'" + vcf + "'") else ""} \
      | bcftools filter -i 'FILTER=="PASS"' \
      -o ~{select_first([outputFilename, "~{basename(vcf, ".vcf")}.filter.vcf"])}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "biocontainers/bcftools:v1.9-1-deb_cv1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "~{basename(vcf, ".vcf")}.filter.vcf"])
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Filter Vardict Somatic Vcf
doc: ''

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: biocontainers/bcftools:v1.9-1-deb_cv1

inputs:
- id: vcf
  label: vcf
  type:
  - File
  - 'null'
  inputBinding:
    position: 1
- id: outputFilename
  label: outputFilename
  type:
  - string
  - 'null'
  default: generated.filter.vcf
  inputBinding:
    prefix: -o
    position: 3
    valueFrom: |-
      $(inputs.vcf ? inputs.vcf.basename.replace(/.vcf$/, "") : "generated").filter.vcf
    shellQuote: false

outputs:
- id: out
  label: out
  type: File
  outputBinding:
    glob: |-
      $(inputs.vcf ? inputs.vcf.basename.replace(/.vcf$/, "") : "generated").filter.vcf
    loadContents: false
stdout: _stdout
stderr: _stderr
arguments:
- position: 0
  valueFrom: "bcftools filter -e 'STATUS=\"GERMLINE\"' -o - "
  shellQuote: false
- position: 2
  valueFrom: "| bcftools filter -i 'FILTER==\"PASS\"'"
  shellQuote: false

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