BCFTools: Sort¶

bcftoolssort · 1 contributor · 1 version

About: Sort VCF/BCF file. Usage: bcftools sort [OPTIONS] <FILE.vcf>

Quickstart¶

from janis_bioinformatics.tools.bcftools.sort.versions import BcfToolsSort_1_9

wf = WorkflowBuilder("myworkflow")

wf.step(
    "bcftoolssort_step",
    BcfToolsSort_1_9(
        vcf=None,
    )
)
wf.output("out", source=bcftoolssort_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 bcftoolssort:

# user inputs
janis inputs bcftoolssort > inputs.yaml

inputs.yaml

vcf: null

Run bcftoolssort with:

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

Information¶

ID:	`bcftoolssort`
URL:	No URL to the documentation was provided
Versions:	v1.9
Container:	biocontainers/bcftools:v1.9-1-deb_cv1
Authors:	Michael Franklin
Citations:	None
Created:	2019-05-09
Updated:	2019-07-11

Outputs¶

name	type	documentation
out	Gzipped<VCF>

Additional configuration (inputs)¶

name	type	prefix	position	documentation
vcf	Union<VCF, Gzipped<VCF>>		1	The VCF file to sort
outputFilename	Optional<Filename>	–output-file		(-o) output file name [stdout]
outputType	Optional<String>	–output-type		(-O) b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]
tempDir	Optional<String>	–temp-dir		(-T) temporary files [/tmp/bcftools-sort.XXXXXX/]

Workflow Description Language¶

version development

task bcftoolssort {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File vcf
    String? outputFilename
    String? outputType
    String? tempDir
  }
  command <<<
    set -e
    bcftools sort \
      --output-file '~{select_first([outputFilename, "generated.sorted.vcf.gz"])}' \
      ~{if defined(select_first([outputType, "z"])) then ("--output-type '" + select_first([outputType, "z"]) + "'") else ""} \
      ~{if defined(tempDir) then ("--temp-dir '" + tempDir + "'") else ""} \
      ~{vcf}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1, 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, 8, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "generated.sorted.vcf.gz"])
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'BCFTools: Sort'
doc: "About:   Sort VCF/BCF file.\nUsage:   bcftools sort [OPTIONS] <FILE.vcf>"

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

inputs:
- id: vcf
  label: vcf
  doc: The VCF file to sort
  type: File
  inputBinding:
    position: 1
- id: outputFilename
  label: outputFilename
  doc: (-o) output file name [stdout]
  type:
  - string
  - 'null'
  default: generated.sorted.vcf.gz
  inputBinding:
    prefix: --output-file
- id: outputType
  label: outputType
  doc: |-
    (-O) b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]
  type: string
  default: z
  inputBinding:
    prefix: --output-type
- id: tempDir
  label: tempDir
  doc: (-T) temporary files [/tmp/bcftools-sort.XXXXXX/]
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --temp-dir

outputs:
- id: out
  label: out
  type: File
  outputBinding:
    glob: generated.sorted.vcf.gz
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- bcftools
- sort
arguments: []

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