What is this?

This is a template to write CWL documents with VSCode with remote container extension.

Requirements

• Visual Studio Code
• Remote - Container extension
• git
• Docker

How to use

• Push the Use this template button in this repository and create a new repository for you,
• Clone it to your local machine, and
• Open the cloned repository with remote container extension of VSCode.
• Have fun!

What is provided by this template?

• A container setting for VSCode. It provides the followings:
  • basic tools such as cwltool, cwl-runner, cwltest and nodejs (for InlineJavascriptRequirement)
  • docker (you can use it without any configurations)
  • Rabix Benten and zatsu-cwl-generator to help writing CWL documents
  • Live Share extension for live coding
• A template for cwltest
• Templates for CI services (described below)

How to run tests

• Edit test.yml
  • Each entry consists of the input CWL file in tool field, the input parameter file in job field and the expected output object in output field (doc field is optional).
  • Here is an example entry:

  - job: job/cat-job.yml
    tool: cwl/cat.cwl
    output:
      out:
        class: File
        basename: output.txt
        checksum: sha1$2af1a59da667eb4aedb182248c1d91741df7e24d
        size: 31
    doc: Template for cwltest

  • You can add new entries for your tools and workflows. I assume that the CWL files are put in cwl directory, the input parameter files are put in job directory, and the example inputs are put in data directory.
• Run test with the following command

  $ cwltest --test test.yml
  Test [1/1] Template for cwltest
  ...
  All tests passed

Supported CI services

This template provides configurations for several CI services. All you have to do is just integrating your repository with CI services. Each CI service executes tests listed in test.yml by using cwltest.

Replace $USER with your account name and $REPO with your repository name.

• Github Actions
  • Replace $WORKFLOW_NAME with your GitHub Actions Workflow name.

  [![Actions Status](https://github.com/$USER/$REPO/workflows/$WORKFLOW_NAME/badge.svg)](https://github.com/$USER/$REPO/actions)

• CircleCI

  [![CircleCI](https://circleci.com/gh/$USER/$REPO.svg?style=shield)](https://circleci.com/gh/$USER/$REPO)

• Gitlab CI

  [![pipeline status](https://gitlab.com/$USER/$REPO/badges/master/pipeline.svg)](https://gitlab.com/$USER/$REPO/commits/master)

TODO

• A tutorial to write CWL
  • Maybe use Zatsu method

License

This repository is licensed under the Unlicense (a.k.a. Public Domain). Under this license, you can:

• freely use the contents,
• freely modify the contents,
• freely change the license, and
• freely distribute it to others!