Sequenza: seqz binning¶

SeqzBinning · 2 contributors · 2 versions

No documentation was provided: contribute one

Quickstart¶

from janis_bioinformatics.tools.sequenza.seqz_binning.versions import SequenzaBinning_3_0_0

wf = WorkflowBuilder("myworkflow")

wf.step(
    "seqzbinning_step",
    SequenzaBinning_3_0_0(
        seqz=None,
        window=None,
    )
)
wf.output("out", source=seqzbinning_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 SeqzBinning:

# user inputs
janis inputs SeqzBinning > inputs.yaml

inputs.yaml

seqz: seqz
window: 0

Run SeqzBinning with:

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

Information¶

ID:	`SeqzBinning`
URL:	http://www.cbs.dtu.dk/biotools/sequenza/
Versions:	3.0.0, 2.2.0.9000
Container:	sequenza/sequenza:3.0.0
Authors:	mumbler, evanwehi
Citations:	None
Created:	2019-12-16
Updated:	2019-12-16

Outputs¶

name	type	documentation
out	File

Additional configuration (inputs)¶

name	type	prefix	position	documentation
seqz	File	–seqz	2	A seqz file.
window	Integer	–window	4	Window size used for binning the original seqz file. Default is 50.
output_filename	Optional<Filename>	-o	6	Output file “-” for STDOUT

Workflow Description Language¶

version development

task SeqzBinning {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File seqz
    Int window
    String? output_filename
  }
  command <<<
    set -e
    sequenza-utils seqz_binning \
      --seqz '~{seqz}' \
      --window ~{window} \
      -o '~{select_first([output_filename, "generated.gz"])}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "sequenza/sequenza:3.0.0"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([output_filename, "generated.gz"])
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'Sequenza: seqz binning'
doc: ''

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: sequenza/sequenza:3.0.0

inputs:
- id: seqz
  label: seqz
  doc: A seqz file.
  type: File
  inputBinding:
    prefix: --seqz
    position: 2
- id: window
  label: window
  doc: Window size used for binning the original seqz file. Default is 50.
  type: int
  inputBinding:
    prefix: --window
    position: 4
- id: output_filename
  label: output_filename
  doc: Output file "-" for STDOUT
  type:
  - string
  - 'null'
  default: generated.gz
  inputBinding:
    prefix: -o
    position: 6

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

baseCommand:
- sequenza-utils
- seqz_binning
arguments: []

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