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

• Copy this repository to your local machine.
• Open the copied repository with remote container extension of VSCode.
• Have fun!

• 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)
• A template for cwltest
• Templates for CI services (described below)

• Edit test.yml
  • Each entry consists of input CWL file in tool field, input parameter file in job field and 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

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.

• Travis CI

  [![Build Status](https://travis-ci.com/$USER/$REPO.svg?branch=master)](https://travis-ci.com/$USER/$REPO)

• 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)

• A tutorial to write CWL
  • Maybe use Zatsu method

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!