BCFTools: Index¶

bcftoolsIndex · 1 contributor · 1 version

Index bgzip compressed VCF/BCF files for random access.

Quickstart¶

from janis_bioinformatics.tools.bcftools.index.versions import BcfToolsIndex_1_9

wf = WorkflowBuilder("myworkflow")

wf.step(
    "bcftoolsindex_step",
    BcfToolsIndex_1_9(
        vcf=None,
    )
)
wf.output("out", source=bcftoolsindex_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 bcftoolsIndex:

# user inputs
janis inputs bcftoolsIndex > inputs.yaml

inputs.yaml

vcf: vcf.vcf.gz

Run bcftoolsIndex with:

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

Information¶

ID:	`bcftoolsIndex`
URL:	https://samtools.github.io/bcftools/bcftools.html#norm
Versions:	v1.9
Container:	biocontainers/bcftools:v1.9-1-deb_cv1
Authors:	Michael Franklin
Citations:	Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, and 1000 Genome Project Data Processing Subgroup, The Sequence alignment/map (SAM) format and SAMtools, Bioinformatics (2009) 25(16) 2078-9
DOI:	http://www.ncbi.nlm.nih.gov/pubmed/19505943
Created:	2019-01-24
Updated:	2019-01-24

Outputs¶

name	type	documentation
out	Gzipped<VCF>

Additional configuration (inputs)¶

name	type	prefix	position	documentation
vcf	Gzipped<VCF>		1
csi	Optional<Boolean>	–csi		(-c) generate CSI-format index for VCF/BCF files [default]
force	Optional<Boolean>	–force		(-f) overwrite index if it already exists
minShift	Optional<Integer>	–min-shift		(-m) set minimal interval size for CSI indices to 2^INT [14]
tbi	Optional<Boolean>	–tbi		(-t) generate TBI-format index for VCF files
threads	Optional<Integer>	–threads		sets the number of threads [0]
nrecords	Optional<Boolean>	–nrecords		(-n) print number of records based on existing index file
stats	Optional<Boolean>	–stats		(-s) print per contig stats based on existing index file

Workflow Description Language¶

version development

task bcftoolsIndex {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File vcf
    Boolean? csi
    Boolean? force
    Int? minShift
    Boolean? tbi
    Int? threads
    Boolean? nrecords
    Boolean? stats
  }
  command <<<
    set -e
    cp -f '~{vcf}' '.'
    bcftools index \
      ~{if (defined(csi) && select_first([csi])) then "--csi" else ""} \
      ~{if (defined(force) && select_first([force])) then "--force" else ""} \
      ~{if defined(minShift) then ("--min-shift " + minShift) else ''} \
      ~{if select_first([tbi, true]) then "--tbi" else ""} \
      ~{if defined(select_first([threads, select_first([runtime_cpu, 1])])) then ("--threads " + select_first([threads, select_first([runtime_cpu, 1])])) else ''} \
      ~{if (defined(nrecords) && select_first([nrecords])) then "--nrecords" else ""} \
      ~{if (defined(stats) && select_first([stats])) then "--stats" else ""} \
      '~{basename(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 = basename(vcf)
    File out_tbi = basename(vcf) + ".tbi"
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'BCFTools: Index'
doc: Index bgzip compressed VCF/BCF files for random access.

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
  listing:
  - entry: $(inputs.vcf)
- class: DockerRequirement
  dockerPull: biocontainers/bcftools:v1.9-1-deb_cv1

inputs:
- id: vcf
  label: vcf
  type: File
  inputBinding:
    position: 1
- id: csi
  label: csi
  doc: (-c) generate CSI-format index for VCF/BCF files [default]
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --csi
- id: force
  label: force
  doc: (-f) overwrite index if it already exists
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --force
- id: minShift
  label: minShift
  doc: (-m) set minimal interval size for CSI indices to 2^INT [14]
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --min-shift
- id: tbi
  label: tbi
  doc: (-t) generate TBI-format index for VCF files
  type: boolean
  default: true
  inputBinding:
    prefix: --tbi
- id: threads
  label: threads
  doc: sets the number of threads [0]
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --threads
    valueFrom: $([inputs.runtime_cpu, 1].filter(function (inner) { return inner !=
      null })[0])
- id: nrecords
  label: nrecords
  doc: (-n) print number of records based on existing index file
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --nrecords
- id: stats
  label: stats
  doc: (-s) print per contig stats based on existing index file
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --stats

outputs:
- id: out
  label: out
  type: File
  secondaryFiles:
  - pattern: .tbi
  outputBinding:
    glob: $(inputs.vcf.basename)
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- bcftools
- index
arguments: []

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