Awk¶

awk · 0 contributors · 1 version

run an awk script

Quickstart¶

from janis_unix.tools.awk import Awk

wf = WorkflowBuilder("myworkflow")

wf.step(
    "awk_step",
    Awk(
        script=None,
        input_files=None,
    )
)
wf.output("out", source=awk_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 awk:

# user inputs
janis inputs awk > inputs.yaml

inputs.yaml

input_files:
- input_files_0
- input_files_1
script: script

Run awk with:

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

Information¶

ID:	`awk`
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
script	File	-f	1
input_files	Array<File>		2

Workflow Description Language¶

version development

task awk {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File script
    Array[File] input_files
  }
  command <<<
    set -e
    awk \
      -f '~{script}' \
      ~{if length(input_files) > 0 then "'" + sep("' '", input_files) + "'" else ""}
  >>>
  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: Awk
doc: run an awk script

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

inputs:
- id: script
  label: script
  type: File
  inputBinding:
    prefix: -f
    position: 1
- id: input_files
  label: input_files
  type:
    type: array
    items: File
  inputBinding:
    position: 2

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

baseCommand: awk
arguments: []

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