Trim IUPAC Bases¶

trimIUPAC · 1 contributor · 2 versions

No documentation was provided: contribute one

Quickstart¶

from janis_bioinformatics.tools.pmac.trimiupac.versions import TrimIUPAC_0_0_5

wf = WorkflowBuilder("myworkflow")

wf.step(
    "trimiupac_step",
    TrimIUPAC_0_0_5(
        vcf=None,
    )
)
wf.output("out", source=trimiupac_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 trimIUPAC:

# user inputs
janis inputs trimIUPAC > inputs.yaml

inputs.yaml

vcf: vcf.vcf

Run trimIUPAC with:

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

Information¶

ID:	`trimIUPAC`
URL:	No URL to the documentation was provided
Versions:	0.0.5, 0.0.4
Container:	michaelfranklin/pmacutil:0.0.5
Authors:	Michael Franklin
Citations:	None
Created:	2019-05-30
Updated:	2019-12-08

Outputs¶

name	type	documentation
out	VCF

Additional configuration (inputs)¶

name	type	prefix	position	documentation
vcf	VCF		0	The VCF to remove the IUPAC bases from
outputFilename	Optional<Filename>		2

Workflow Description Language¶

version development

task trimIUPAC {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File vcf
    String? outputFilename
  }
  command <<<
    set -e
    trimIUPAC.py \
      '~{vcf}' \
      '~{select_first([outputFilename, "generated.trimmed.vcf"])}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "michaelfranklin/pmacutil:0.0.5"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 1, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "generated.trimmed.vcf"])
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Trim IUPAC Bases
doc: ''

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: michaelfranklin/pmacutil:0.0.5

inputs:
- id: vcf
  label: vcf
  doc: The VCF to remove the IUPAC bases from
  type: File
  inputBinding:
    position: 0
- id: outputFilename
  label: outputFilename
  type:
  - string
  - 'null'
  default: generated.trimmed.vcf
  inputBinding:
    position: 2

outputs:
- id: out
  label: out
  type: File
  outputBinding:
    glob: generated.trimmed.vcf
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand: trimIUPAC.py
arguments: []

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