UncompressArchive

UncompressArchive · 0 contributors · 1 version

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Quickstart

from janis_unix.tools.uncompressarchive import UncompressArchive

wf = WorkflowBuilder("myworkflow")

wf.step(
    "uncompressarchive_step",
    UncompressArchive(
        file=None,
    )
)
wf.output("out", source=uncompressarchive_step.out)

OR

1. Install Janis
2. Ensure Janis is configured to work with Docker or Singularity.
3. Ensure all reference files are available:

Note

More information about these inputs are available below.

4. Generate user input files for UncompressArchive:

# user inputs
janis inputs UncompressArchive > inputs.yaml

inputs.yaml

file: file.gz

5. Run UncompressArchive with:

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

Information

ID:UncompressArchive 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	stdout<File>

Additional configuration (inputs)

name	type	prefix	position	documentation
file	Gzipped<File>		1
stdout	Optional<Boolean>	-c		write on standard output, keep original files unchanged
decompress	Optional<Boolean>	-d		decompress
force	Optional<Boolean>	-f		force overwrite of output file and compress links
keep	Optional<Boolean>	-k		keep (don’t delete) input files
list	Optional<Boolean>	-l		list compressed file contents
noName	Optional<Boolean>	-n		do not save or restore the original name and time stamp
name	Optional<Boolean>	-N		save or restore the original name and time stamp
quiet	Optional<Boolean>	-q		suppress all warnings
recursive	Optional<Boolean>	-r		operate recursively on directories
suffix	Optional<String>	-s		use suffix SUF on compressed files
test	Optional<Boolean>	-t		test compressed file integrity
fast	Optional<Boolean>	-1		compress faster
best	Optional<Boolean>	-9		compress better
rsyncable	Optional<Boolean>	–rsyncable		Make rsync-friendly archive

Workflow Description Language

version development

task UncompressArchive {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File file
    Boolean? stdout
    Boolean? decompress
    Boolean? force
    Boolean? keep
    Boolean? list
    Boolean? noName
    Boolean? name
    Boolean? quiet
    Boolean? recursive
    String? suffix
    Boolean? test
    Boolean? fast
    Boolean? best
    Boolean? rsyncable
  }
  command <<<
    set -e
    gunzip \
      ~{if select_first([stdout, true]) then "-c" else ""} \
      ~{if (defined(decompress) && select_first([decompress])) then "-d" else ""} \
      ~{if (defined(force) && select_first([force])) then "-f" else ""} \
      ~{if (defined(keep) && select_first([keep])) then "-k" else ""} \
      ~{if (defined(list) && select_first([list])) then "-l" else ""} \
      ~{if (defined(noName) && select_first([noName])) then "-n" else ""} \
      ~{if (defined(name) && select_first([name])) then "-N" else ""} \
      ~{if (defined(quiet) && select_first([quiet])) then "-q" else ""} \
      ~{if (defined(recursive) && select_first([recursive])) then "-r" else ""} \
      ~{if defined(suffix) then ("-s '" + suffix + "'") else ""} \
      ~{if (defined(test) && select_first([test])) then "-t" else ""} \
      ~{if (defined(fast) && select_first([fast])) then "-1" else ""} \
      ~{if (defined(best) && select_first([best])) then "-9" else ""} \
      ~{if (defined(rsyncable) && select_first([rsyncable])) then "--rsyncable" else ""} \
      '~{file}'
  >>>
  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 {
    File out = stdout()
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: UncompressArchive

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

inputs:
- id: file
  label: file
  type: File
  inputBinding:
    position: 1
- id: stdout
  label: stdout
  doc: write on standard output, keep original files unchanged
  type: boolean
  default: true
  inputBinding:
    prefix: -c
- id: decompress
  label: decompress
  doc: decompress
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -d
- id: force
  label: force
  doc: force overwrite of output file and compress links
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -f
- id: keep
  label: keep
  doc: keep (don't delete) input files
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -k
- id: list
  label: list
  doc: list compressed file contents
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -l
- id: noName
  label: noName
  doc: do not save or restore the original name and time stamp
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -n
- id: name
  label: name
  doc: save or restore the original name and time stamp
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -N
- id: quiet
  label: quiet
  doc: suppress all warnings
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -q
- id: recursive
  label: recursive
  doc: operate recursively on directories
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -r
- id: suffix
  label: suffix
  doc: use suffix SUF on compressed files
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -s
- id: test
  label: test
  doc: test compressed file integrity
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -t
- id: fast
  label: fast
  doc: compress faster
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: '-1'
- id: best
  label: best
  doc: compress better
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: '-9'
- id: rsyncable
  label: rsyncable
  doc: Make rsync-friendly archive
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --rsyncable

outputs:
- id: out
  label: out
  type: stdout
stdout: _stdout
stderr: _stderr

baseCommand: gunzip
arguments: []

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