Tar (unarchive)¶

untar · 0 contributors · 1 version

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Quickstart¶

from janis_unix.tools.untar import Untar

wf = WorkflowBuilder("myworkflow")

wf.step(
    "untar_step",
    Untar(
        tarfile=None,
    )
)
wf.output("out", source=untar_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 untar:

# user inputs
janis inputs untar > inputs.yaml

inputs.yaml

tarfile: tarfile.tar

Run untar with:

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

Information¶

ID:	`untar`
URL:	No URL to the documentation was provided
Versions:	v1.0.0
Container:	ubuntu@sha256:1d7b639619bdca2d008eca2d5293e3c43ff84cbee597ff76de3b7a7de3e84956
Authors:
Citations:	None
Created:	None
Updated:	None

Outputs¶

name	type	documentation
out	Array<File>

Additional configuration (inputs)¶

name	type	prefix	position	documentation
tarfile	TarFile		0

Workflow Description Language¶

version development

task untar {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File tarfile
  }
  command <<<
    set -e
    tar xf \
      '~{tarfile}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "ubuntu@sha256:1d7b639619bdca2d008eca2d5293e3c43ff84cbee597ff76de3b7a7de3e84956"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    Array[File] out = glob("*.java")
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Tar (unarchive)

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: ubuntu@sha256:1d7b639619bdca2d008eca2d5293e3c43ff84cbee597ff76de3b7a7de3e84956

inputs:
- id: tarfile
  label: tarfile
  type: File
  inputBinding:
    position: 0

outputs:
- id: out
  label: out
  type:
    type: array
    items: File
  outputBinding:
    glob: '*.java'
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- tar
- xf
arguments: []

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