Add Sym to DepthOfCoverage¶

addSymToDepthOfCoverage · 1 contributor · 1 version

usage: add_sym_to_DepthOfCoverage.py [-h] -i INPUT -o OUTPUT -bed BED

Performance summary of bam

optional arguments:

`-h, --help`	show this help message and exit
`-i INPUT`	Gatk3 DepthOfCoverage interval_summary output
`-o OUTPUT`	Output file name

-bed BED Annotated bed file

Quickstart¶

from janis_bioinformatics.tools.pmac.addsymtodepthofcoverage.versions import AddSymToDepthOfCoverage_0_0_7

wf = WorkflowBuilder("myworkflow")

wf.step(
    "addsymtodepthofcoverage_step",
    AddSymToDepthOfCoverage_0_0_7(
        inputFile=None,
        bed=None,
    )
)
wf.output("out", source=addsymtodepthofcoverage_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 addSymToDepthOfCoverage:

# user inputs
janis inputs addSymToDepthOfCoverage > inputs.yaml

inputs.yaml

bed: bed.bed
inputFile: inputFile

Run addSymToDepthOfCoverage with:

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

Information¶

ID:	`addSymToDepthOfCoverage`
URL:	https://github.com/PMCC-BioinformaticsCore/scripts/tree/master/performance
Versions:	0.0.7
Container:	michaelfranklin/pmacutil:0.0.7
Authors:	Jiaan Yu
Citations:	None
Created:	2020-04-09 00:00:00
Updated:	2020-04-09 00:00:00

Outputs¶

name	type	documentation
out	TextFile

Additional configuration (inputs)¶

name	type	prefix	documentation
inputFile	File	-i	Gatk3 DepthOfCoverage interval_summary output
bed	bed	-bed	Annotated bed file
outputFilename	Optional<Filename>	-o	Output file name

Workflow Description Language¶

version development

task addSymToDepthOfCoverage {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File inputFile
    String? outputFilename
    File bed
  }
  command <<<
    set -e
    add_sym_to_DepthOfCoverage.py \
      -i '~{inputFile}' \
      -o '~{select_first([outputFilename, "generated.txt"])}' \
      -bed '~{bed}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "michaelfranklin/pmacutil:0.0.7"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "generated.txt"])
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Add Sym to DepthOfCoverage
doc: |-
  usage: add_sym_to_DepthOfCoverage.py [-h] -i INPUT -o OUTPUT -bed BED

  Performance summary of bam

  optional arguments:
    -h, --help  show this help message and exit
    -i INPUT    Gatk3 DepthOfCoverage interval_summary output
    -o OUTPUT   Output file name
    -bed BED    Annotated bed file


requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: michaelfranklin/pmacutil:0.0.7

inputs:
- id: inputFile
  label: inputFile
  doc: Gatk3 DepthOfCoverage interval_summary output
  type: File
  inputBinding:
    prefix: -i
- id: outputFilename
  label: outputFilename
  doc: Output file name
  type:
  - string
  - 'null'
  default: generated.txt
  inputBinding:
    prefix: -o
- id: bed
  label: bed
  doc: Annotated bed file
  type: File
  inputBinding:
    prefix: -bed

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

baseCommand: add_sym_to_DepthOfCoverage.py
arguments: []

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