Echo¶

echo · 0 contributors · 1 version

The echo utility writes any specified operands, separated by single blank (` ‘) characters and followed by a newline (` ‘) character, to the standard output.

Some shells may provide a builtin echo command which is similar or identical to this utility. Most notably, the builtin echo in sh(1) does not accept the -n option. Consult the builtin(1) manual page.

Quickstart¶

from janis_unix.tools.echo import Echo

wf = WorkflowBuilder("myworkflow")

wf.step(
    "echo_step",
    Echo(
        inp=None,
    )
)
wf.output("out", source=echo_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 echo:

# user inputs
janis inputs echo > inputs.yaml

inputs.yaml

inp: <value>

Run echo with:

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

Information¶

ID:	`echo`
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
inp	String		1
include_newline	Optional<Boolean>	-n		Do not print the trailing newline character. This may also be achieved by appending `c’ to the end of the string, as is done by iBCS2 compatible systems. Note that this option as well as the effect of `c’ are implementation-defined in IEEE Std 1003.1-2001 (``POSIX.1’’) as amended by Cor. 1-2002. Applications aiming for maximum portability are strongly encouraged to use printf(1) to suppress the newline character.

Workflow Description Language¶

version development

task echo {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    String inp
    Boolean? include_newline
  }
  command <<<
    set -e
    echo \
      ~{if (defined(include_newline) && select_first([include_newline])) then "-n" else ""} \
      '~{inp}'
  >>>
  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, 60, 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: Echo
doc: |-
  The echo utility writes any specified operands, separated by single blank (` ') characters and followed by a newline (`
  ') character, to the standard output.

  Some shells may provide a builtin echo command which is similar or identical to this utility. Most notably, the builtin echo in sh(1) does not accept the -n option. Consult the builtin(1) manual page.

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

inputs:
- id: inp
  label: inp
  type: string
  inputBinding:
    position: 1
- id: include_newline
  label: include_newline
  doc: |-
    Do not print the trailing newline character.  This may also be achieved by appending `\c' to the end of the string, as is done by iBCS2 compatible systems.  Note that this option as well as the effect of `\c' are implementation-defined in IEEE Std 1003.1-2001 (``POSIX.1'') as amended by Cor. 1-2002.  Applications aiming for maximum portability are strongly encouraged to use printf(1) to suppress the newline character.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -n

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

baseCommand: echo
arguments: []

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 60, 86400].filter(function (inner) { return inner != null })[0])
id: echo