Hello, World!¶

hello · 1 contributor · 1 version

This is the ‘Hello, world’ equivalent workflow that uses the Echo unix tool to log “Hello, World!” to the console, and collects the result.

This is designed to be the first example that you can run with janis, ie:

janis run hello

Quickstart¶

from janis_unix.tools.hello import HelloWorkflow

wf = WorkflowBuilder("myworkflow")

wf.step(
    "hello_step",
    HelloWorkflow(

    )
)
wf.output("out", source=hello_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 hello:

# user inputs
janis inputs hello > inputs.yaml

inputs.yaml

{}

Run hello with:

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

Information¶

URL: No URL to the documentation was provided

ID:	`hello`
URL:	No URL to the documentation was provided
Versions:	v1.0.0
Authors:	Michael Franklin
Citations:
Created:	None
Updated:	2019-08-12

Outputs¶

name	type	documentation
out	File

Workflow¶

Embedded Tools¶

Echo	`echo/v1.0.0`

Additional configuration (inputs)¶

name	type	documentation
inp	Optional<String>

Workflow Description Language¶

version development

import "tools/echo_v1_0_0.wdl" as E

workflow hello {
  input {
    String? inp = "Hello, world!"
  }
  call E.echo as hello {
    input:
      inp=select_first([inp, "Hello, world!"])
  }
  output {
    File out = hello.out
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: Hello, World!
doc: |
  This is the 'Hello, world' equivalent workflow that uses the Echo unix
  tool to log "Hello, World!" to the console, and collects the result.

  This is designed to be the first example that you can run with janis, ie:

  ``janis run hello``

requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement

inputs:
- id: inp
  type: string
  default: Hello, world!

outputs:
- id: out
  type: File
  outputSource: hello/out

steps:
- id: hello
  label: Echo
  in:
  - id: inp
    source: inp
  run: tools/echo_v1_0_0.cwl
  out:
  - id: out
id: hello