biobb/cwl_dind repository overview

⁠Docker-in-Docker CWL container

In this repository you can find a docker container prepared for executing CWL BioBB workflows inside.

⁠Installation

First off, download the image into your computer.

⁠AMD architecture

docker pull biobb/cwl_dind:amd64

⁠ARM architecture

docker pull biobb/cwl_dind:arm64

⁠Setup

Please have the following data in the folder where the docker will be run:

• Input(s) needed for the workflow execution.
• BioBB adapters. For executing BioBB CWL workflows is needed to have the BioBB adapters⁠ for this concrete workflow.
• workflow.cwl: the CWL file with all the steps to execute this workflow.
• workflow_input_descriptions.yml: the configuration file with the I/O dependencies and settings for each step of the workflow.

⁠Run workflow

Be sure to execute the following instructions in the same folder where the files described in the setup section are.

⁠AMD architecture

docker run --privileged -d --name my_container -v /path/to/files:/workspace biobb/cwl_dind:amd64
docker exec -w /workspace my_container cwltool --tmpdir-prefix /workspace/tmpd- workflow.cwl workflow_input_descriptions.yml

Where /path/to/files is the folder where the files described in the setup section are.

⁠ARM architecture

docker run --privileged -d --name my_container -v /path/to/files:/workspace biobb/cwl_dind:arm64
docker exec -w /workspace my_container cwltool --tmpdir-prefix /workspace/tmpd- workflow.cwl workflow_input_descriptions.yml

Where /path/to/files is the folder where the files described in the setup section are.

⁠Get output results

Once the workflow finishes its execution (it can take a while depending on the workflow and / or the parameters given to it), the outputs will be found in the same folder where the files described in the setup section are.