VcfLib: Vcf Length¶
vcflength
· 1 contributor · 1 version
Adds the length of the variant record (in [-/+]) relative to the reference allele to each VCF record.
Quickstart¶
from janis_bioinformatics.tools.vcflib.vcflength.versions import VcfLength_1_0_1 wf = WorkflowBuilder("myworkflow") wf.step( "vcflength_step", VcfLength_1_0_1( vcf=None, ) ) wf.output("out", source=vcflength_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 vcflength:
# user inputs
janis inputs vcflength > inputs.yaml
inputs.yaml
vcf: vcf.vcf
- Run vcflength with:
janis run [...run options] \
--inputs inputs.yaml \
vcflength
Information¶
ID: | vcflength |
---|---|
URL: | https://github.com/vcflib/vcflib |
Versions: | v1.0.1 |
Container: | shollizeck/vcflib:1.0.1 |
Authors: | Michael Franklin |
Citations: | None |
Created: | 2020-06-04 |
Updated: | 2020-06-04 |
Outputs¶
name | type | documentation |
---|---|---|
out | stdout<VCF> | VCF with length of the variant record added to each record |
Additional configuration (inputs)¶
name | type | prefix | position | documentation |
---|---|---|---|---|
vcf | VCF | 1 | VCF to add length of variant record relative to the reference allele to. |
Workflow Description Language¶
version development
task vcflength {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
File vcf
}
command <<<
set -e
vcflength \
'~{vcf}'
>>>
runtime {
cpu: select_first([runtime_cpu, 1])
disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
docker: "shollizeck/vcflib:1.0.1"
duration: select_first([runtime_seconds, 86400])
memory: "~{select_first([runtime_memory, 4])}G"
preemptible: 2
}
output {
File out = stdout()
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'VcfLib: Vcf Length'
doc: |-
Adds the length of the variant record (in [-/+]) relative to the reference allele to each VCF record.
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: shollizeck/vcflib:1.0.1
inputs:
- id: vcf
label: vcf
doc: VCF to add length of variant record relative to the reference allele to.
type: File
inputBinding:
position: 1
outputs:
- id: out
label: out
doc: VCF with length of the variant record added to each record
type: stdout
stdout: _stdout
stderr: _stderr
baseCommand: vcflength
arguments: []
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: vcflength