IGVTools: Index Features¶

IgvToolsIndexFeatures · 1 contributor · 1 version

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Quickstart¶

from janis_bioinformatics.tools.igvtools.index.versions import IgvIndexFeature_2_5_3

wf = WorkflowBuilder("myworkflow")

wf.step(
    "igvtoolsindexfeatures_step",
    IgvIndexFeature_2_5_3(
        inp=None,
    )
)
wf.output("out", source=igvtoolsindexfeatures_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 IgvToolsIndexFeatures:

# user inputs
janis inputs IgvToolsIndexFeatures > inputs.yaml

inputs.yaml

inp: inp.vcf

Run IgvToolsIndexFeatures with:

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

Information¶

ID:	`IgvToolsIndexFeatures`
URL:	No URL to the documentation was provided
Versions:	2.5.3
Container:	quay.io/biocontainers/igvtools:2.5.3–0
Authors:	Michael Franklin
Citations:	None
Created:	2020-06-04
Updated:	2020-06-15

Outputs¶

name	type	documentation
out	IndexedVCF

Additional configuration (inputs)¶

name	type	prefix	position	documentation
inp	VCF		1

Workflow Description Language¶

version development

task IgvToolsIndexFeatures {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File inp
  }
  command <<<
    set -e
    cp -f '~{inp}' 'sample.vcf'
    igvtools index \
      sample.vcf
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "quay.io/biocontainers/igvtools:2.5.3--0"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = "sample.vcf"
    File out_idx = "sample.vcf" + ".idx"
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'IGVTools: Index Features'
doc: ''

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
  listing:
  - entryname: sample.vcf
    entry: $(inputs.inp)
- class: DockerRequirement
  dockerPull: quay.io/biocontainers/igvtools:2.5.3--0

inputs:
- id: inp
  label: inp
  type: File
  inputBinding:
    position: 1

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

baseCommand:
- igvtools
- index
arguments: []

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