maurya-anand/wdl-qc

Fastq file QC and trimming using WDL

WDL Pipeline for QC

This repo is for testing purposes only.

Tasks

• Publishing on dockstore
• Versioning and tags for the pipeline and the container
• Testing Github actions CI/CD
  • Automatic credential management (github + container registry)
  • Extract metadata from the repo to assign tags and releases
  • Automatically build and push the container to ghcr.io. (container)
  • Create a git repo release from the tags. (releases)
• Documenting tags, releases and change logs for the pipelines
• Container security
• Adding custom scripts and executables
• Explore other container registry for private hosting

Prerequisites

• Mamba
• Docker

Setting up the test environment

$ mamba create -n cromwell
$ mamba activate cromwell
(cromwell) $ mamba install cromwell

Example usage

(cromwell) $ cromwell run workflows/run-qc.wdl -i example/inputs.json

Docs

• Changelog
• License