VcfLib: VcfStreamSort¶
vcfstreamsort
· 1 contributor · 1 version
usage: vcfallelicprimitives [options] [file]
- options:
-m, --use-mnps Retain MNPs as separate events (default: false) -t, --tag-parsed FLAG Tag records which are split apart of a complex allele with this flag
Quickstart¶
from janis_bioinformatics.tools.vcflib.vcfstreamsort.versions import VcfStreamSort_1_0_1 wf = WorkflowBuilder("myworkflow") wf.step( "vcfstreamsort_step", VcfStreamSort_1_0_1( vcf=None, ) ) wf.output("out", source=vcfstreamsort_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 vcfstreamsort:
# user inputs
janis inputs vcfstreamsort > inputs.yaml
inputs.yaml
vcf: vcf.vcf
- Run vcfstreamsort with:
janis run [...run options] \
--inputs inputs.yaml \
vcfstreamsort
Information¶
ID: | vcfstreamsort |
---|---|
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 | VCF | 3 | ||
inMemoryFlag | Optional<Boolean> | -a | load all sites and then sort in memory | |
windowSize | Optional<Integer> | -w | number of sites to sort (default 10000) |
Workflow Description Language¶
version development
task vcfstreamsort {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
File vcf
Boolean? inMemoryFlag
Int? windowSize
}
command <<<
set -e
vcfstreamsort \
~{if select_first([inMemoryFlag, false]) then "-a" else ""} \
~{if defined(windowSize) then ("-w " + windowSize) else ''} \
'~{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: VcfStreamSort'
doc: |-
usage: vcfallelicprimitives [options] [file]
options:
-m, --use-mnps Retain MNPs as separate events (default: false)
-t, --tag-parsed FLAG Tag records which are split apart of a complex allele with this flag
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: shollizeck/vcflib:1.0.1
inputs:
- id: vcf
label: vcf
type: File
inputBinding:
position: 3
- id: inMemoryFlag
label: inMemoryFlag
doc: load all sites and then sort in memory
type: boolean
default: false
inputBinding:
prefix: -a
- id: windowSize
label: windowSize
doc: number of sites to sort (default 10000)
type:
- int
- 'null'
inputBinding:
prefix: -w
outputs:
- id: out
label: out
doc: VCF output
type: stdout
stdout: _stdout
stderr: _stderr
baseCommand: vcfstreamsort
arguments: []
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: vcfstreamsort