Split Multiple Alleles and Normalise Vcf¶
SplitMultiAlleleNormaliseVcf
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Quickstart¶
from janis_bioinformatics.tools.common.splitmultiallele_normalistvcf import SplitMultiAlleleNormaliseVcf wf = WorkflowBuilder("myworkflow") wf.step( "splitmultiallelenormalisevcf_step", SplitMultiAlleleNormaliseVcf( reference=None, ) ) wf.output("out", source=splitmultiallelenormalisevcf_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 SplitMultiAlleleNormaliseVcf:
# user inputs
janis inputs SplitMultiAlleleNormaliseVcf > inputs.yaml
inputs.yaml
reference: reference.fasta
- Run SplitMultiAlleleNormaliseVcf with:
janis run [...run options] \
--inputs inputs.yaml \
SplitMultiAlleleNormaliseVcf
Information¶
ID: | SplitMultiAlleleNormaliseVcf |
---|---|
URL: | No URL to the documentation was provided |
Versions: | v0.5772 |
Container: | heuermh/vt |
Authors: | Jiaan Yu |
Citations: | None |
Created: | 2020-06-04 |
Updated: | 2020-06-04 |
Outputs¶
name | type | documentation |
---|---|---|
out | VCF |
Additional configuration (inputs)¶
name | type | prefix | position | documentation |
---|---|---|---|---|
reference | FastaWithIndexes | -r | 4 | |
vcf | Optional<VCF> | 1 | ||
compressedTabixVcf | Optional<Gzipped<VCF>> | 1 | ||
compressedVcf | Optional<Gzipped<VCF>> | 1 | ||
outputFilename | Optional<Filename> | -o | 6 |
Workflow Description Language¶
version development
task SplitMultiAlleleNormaliseVcf {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
File? vcf
File? compressedTabixVcf
File? compressedTabixVcf_tbi
File? compressedVcf
File reference
File reference_fai
File reference_amb
File reference_ann
File reference_bwt
File reference_pac
File reference_sa
File reference_dict
String? outputFilename
}
command <<<
set -e
\
vt decompose -s \
~{vcf} \
~{compressedTabixVcf} \
~{compressedVcf} \
| vt normalize -n -q - \
-r ~{reference} \
-o ~{select_first([outputFilename, "generated.norm.vcf"])}
>>>
runtime {
cpu: select_first([runtime_cpu, 1, 1])
disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
docker: "heuermh/vt"
duration: select_first([runtime_seconds, 86400])
memory: "~{select_first([runtime_memory, 8, 4])}G"
preemptible: 2
}
output {
File out = select_first([outputFilename, "generated.norm.vcf"])
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Split Multiple Alleles and Normalise Vcf
doc: ''
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: heuermh/vt
inputs:
- id: vcf
label: vcf
type:
- File
- 'null'
inputBinding:
position: 1
shellQuote: false
- id: compressedTabixVcf
label: compressedTabixVcf
type:
- File
- 'null'
secondaryFiles:
- pattern: .tbi
inputBinding:
position: 1
shellQuote: false
- id: compressedVcf
label: compressedVcf
type:
- File
- 'null'
inputBinding:
position: 1
shellQuote: false
- id: reference
label: reference
type: File
secondaryFiles:
- pattern: .fai
- pattern: .amb
- pattern: .ann
- pattern: .bwt
- pattern: .pac
- pattern: .sa
- pattern: ^.dict
inputBinding:
prefix: -r
position: 4
shellQuote: false
- id: outputFilename
label: outputFilename
type:
- string
- 'null'
default: generated.norm.vcf
inputBinding:
prefix: -o
position: 6
shellQuote: false
outputs:
- id: out
label: out
type: File
outputBinding:
glob: generated.norm.vcf
loadContents: false
stdout: _stdout
stderr: _stderr
arguments:
- position: 0
valueFrom: 'vt decompose -s '
shellQuote: false
- position: 2
valueFrom: '| vt normalize -n -q - '
shellQuote: false
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: SplitMultiAlleleNormaliseVcf