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A template to write CWL documents with VSCode with remote container extension
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README.md

What is this?

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

Build Status Actions Status CircleCI pipeline status

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.
  • 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:
  • 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.

  • Travis CI Build Status
    [![Build Status](https://travis-ci.com/$USER/$REPO.svg?branch=master)](https://travis-ci.com/$USER/$REPO)
  • Github Actions Actions Status
    • 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
    [![CircleCI](https://circleci.com/gh/$USER/$REPO.svg?style=shield)](https://circleci.com/gh/$USER/$REPO)
  • Gitlab CI pipeline status
    [![pipeline status](https://gitlab.com/$USER/$REPO/badges/master/pipeline.svg)](https://gitlab.com/$USER/$REPO/commits/master)

TODO

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!
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