Solving more complex problems with scripts and toolkits

Overview

Teaching: 0 min
Exercises: 0 min

Questions

• How to include and run a script in a step at runtime?

• Which requirements need to be specified?

• How to capture output of a script?

• How to find other tools/solutions for awkward problems?

Objectives

• script objectives:

• Include and run a script in a step at runtime

• Capture output of a script

• tools objectives:

• know good resources for finding solutions to common problems

By the end of this episode, learners should be able to include and run their own script in a step at runtime and be aware of where they can look for CWL recipes and more help for common, but awkward, tasks.

Exercise 1:

Which Requirement from the following options is used to create a script at runtime?

A. InlineJavascriptRequirement
B. InitialWorkDirRequirement
C. ResourceRequirement
D. DockerRequirement

Solution

B. InitialWorkDirRequirement

Exercise 2:

Using the template below, add the missing instructions so that a script named script.sh with the specified contents is created at runtime.

InitialWorkDirRequirement:
  listing:
    - ------: script.sh
      ------: |
        echo "*Documenting input*" && \
        echo "Input received: $(inputs.message)" && \
        echo "Exit"

inputs:
  message:
    type: string

Solution:

InitialWorkDirRequirement:
  listing:
    - entryname: script.sh
      entry: |
        echo "*Documenting input*" && \
        echo "Input received: $(inputs.message)" && \
        echo "Exit"

inputs:
  message:
    type: string

Exercise 3:

Since we are using echo in the script (as shown below) - what is the appropriate type in the outputs section of following code block to capture standard output?

class: CommandLineTool
cwlVersion: v1.1
requirements:
  DockerRequirement:
    dockerPull: 'debian:stable'
  InitialWorkDirRequirement:
    listing:
      - entryname: script.sh
        entry: |
          echo "*Documenting input*" && \
          echo "Input received: $(inputs.message)" && \
          echo "Exit"

inputs:
  message:
    type: string

stdout: "message.txt"

outputs:
 message:
   type: ----

Your options are: A. File B. Directory C. stdout D. string

Solution:

C. stdout

Exercise 4:

Fix the baseCommand in following code snippet to execute the script we have created in previous exercises.

baseCommand: []

Solution:

baseCommand: [ sh, script.sh ]

Exercise 5:

CHALLENGE question. Extend the outputs section of the following CWLtool definition to capture the script we have created along with tools’ standard output.

This will help you inspect the generated script and is useful in more complex situations to troubleshoot related issues.

class: CommandLineTool
cwlVersion: v1.1
requirements:
  DockerRequirement:
    dockerPull: 'debian:stable'
  InitialWorkDirRequirement:
    listing:
      - entryname: script.sh
        entry: |
          echo "*Documenting input*" && \
          echo "Input received: $(inputs.message)" && \
          echo "Exit"

inputs:
  message:
    type: string

stdout: "message.txt"
baseCommand: ["sh", "script.sh"]

outputs:
  message:
    type: stdout

Solution:

class: CommandLineTool
cwlVersion: v1.1
requirements:
  DockerRequirement:
    dockerPull: 'debian:stable'
  InitialWorkDirRequirement:
    listing:
      - entryname: script.sh
        entry: |
          echo "*Documenting input*" && \
          echo "Input received: $(inputs.message)" && \
          echo "Exit"

inputs:
  message:
    type: string

stdout: "message.txt"
baseCommand: ["sh", "script.sh"]

outputs:
  message:
    type: stdout
  script:
    type: File
    outputBinding:
      glob: "script.sh"

Key Points

• First key point. Brief Answer to questions. (FIXME)