VcfLib: VcfUniq¶
vcfuniq
· 1 contributor · 1 version
usage: vcffuniq [file] Like GNU uniq, but for VCF records. Remove records which have the same positon, ref, and alt as the previous record.
Quickstart¶
from janis_bioinformatics.tools.vcflib.vcfuniq.versions import VcfUniq_1_0_1 wf = WorkflowBuilder("myworkflow") wf.step( "vcfuniq_step", VcfUniq_1_0_1( vcf=None, ) ) wf.output("out", source=vcfuniq_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 vcfuniq:
# user inputs
janis inputs vcfuniq > inputs.yaml
inputs.yaml
vcf: vcf.vcf.gz
- Run vcfuniq with:
janis run [...run options] \
--inputs inputs.yaml \
vcfuniq
Information¶
ID: | vcfuniq |
---|---|
URL: | https://github.com/vcflib/vcflib |
Versions: | v1.0.1 |
Container: | shollizeck/vcflib:1.0.1 |
Authors: | Sebastian Hollizeck |
Citations: | None |
Created: | 2019-10-18 |
Updated: | 2019-10-18 |
Outputs¶
name | type | documentation |
---|---|---|
out | stdout<VCF> | VCF output |
Additional configuration (inputs)¶
name | type | prefix | position | documentation |
---|---|---|---|---|
vcf | Gzipped<VCF> | 3 |
Workflow Description Language¶
version development
task vcfuniq {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
File vcf
}
command <<<
set -e
vcfuniq \
'~{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: VcfUniq'
doc: |-
usage: vcffuniq [file]
Like GNU uniq, but for VCF records. Remove records which have the same positon, ref, and alt as the previous record.
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: shollizeck/vcflib:1.0.1
inputs:
- id: vcf
label: vcf
type: File
inputBinding:
position: 3
outputs:
- id: out
label: out
doc: VCF output
type: stdout
stdout: _stdout
stderr: _stderr
baseCommand: vcfuniq
arguments: []
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: vcfuniq