Concat Strelka Somatic Vcf¶

ConcatStrelkaSomaticVcf · 1 contributor · 1 version

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Quickstart¶

from janis_bioinformatics.tools.common.concat_strelkasomaticvcf import ConcatStrelkaSomaticVcf

wf = WorkflowBuilder("myworkflow")

wf.step(
    "concatstrelkasomaticvcf_step",
    ConcatStrelkaSomaticVcf(
        headerVcfs=None,
        contentVcfs=None,
    )
)
wf.output("out", source=concatstrelkasomaticvcf_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 ConcatStrelkaSomaticVcf:

# user inputs
janis inputs ConcatStrelkaSomaticVcf > inputs.yaml

inputs.yaml

contentVcfs:
- contentVcfs_0.vcf.gz
- contentVcfs_1.vcf.gz
headerVcfs:
- headerVcfs_0.vcf.gz
- headerVcfs_1.vcf.gz

Run ConcatStrelkaSomaticVcf with:

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

Information¶

ID:	`ConcatStrelkaSomaticVcf`
URL:	No URL to the documentation was provided
Versions:	0.1.16
Container:	biocontainers/vcftools:v0.1.16-1-deb_cv1
Authors:	Jiaan Yu
Citations:	None
Created:	2020-06-04
Updated:	2020-07-29

Outputs¶

name	type	documentation
out	VCF

Additional configuration (inputs)¶

name	type	prefix	position
headerVcfs	Array<Gzipped<VCF>>		1
contentVcfs	Array<Gzipped<VCF>>		4
outputFilename	Optional<Filename>	>	6

Workflow Description Language¶

version development

task ConcatStrelkaSomaticVcf {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Array[File] headerVcfs
    Array[File] headerVcfs_tbi
    Array[File] contentVcfs
    Array[File] contentVcfs_tbi
    String? outputFilename
  }
  command <<<
    set -e
     \
      vcf-merge \
      ~{if length(headerVcfs) > 0 then "'" + sep("' '", headerVcfs) + "'" else ""} \
      | grep '^##' > header.vcf; \
      vcf-concat \
      ~{if length(contentVcfs) > 0 then "'" + sep("' '", contentVcfs) + "'" else ""} \
      | grep -v '^##' > content.vcf; cat header.vcf content.vcf \
      > ~{select_first([outputFilename, "generated.strelka.vcf"])}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "biocontainers/vcftools:v0.1.16-1-deb_cv1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "generated.strelka.vcf"])
  }
}

Common Workflow Language¶

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

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: biocontainers/vcftools:v0.1.16-1-deb_cv1

inputs:
- id: headerVcfs
  label: headerVcfs
  type:
    type: array
    items: File
  inputBinding:
    position: 1
- id: contentVcfs
  label: contentVcfs
  type:
    type: array
    items: File
  inputBinding:
    position: 4
- id: outputFilename
  label: outputFilename
  type:
  - string
  - 'null'
  default: generated.strelka.vcf
  inputBinding:
    prefix: '>'
    position: 6
    shellQuote: false

outputs:
- id: out
  label: out
  type: File
  outputBinding:
    glob: generated.strelka.vcf
    loadContents: false
stdout: _stdout
stderr: _stderr
arguments:
- position: 0
  valueFrom: vcf-merge
  shellQuote: false
- position: 2
  valueFrom: "| grep '^##' > header.vcf;"
  shellQuote: false
- position: 3
  valueFrom: vcf-concat
  shellQuote: false
- position: 5
  valueFrom: "| grep -v '^##' > content.vcf; cat header.vcf content.vcf"
  shellQuote: false

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