pancancer/broad_wrapper_workflow repository overview

⁠BroadWrapperWorkflow

A SeqWare workflow that wraps the Broad workflow.

⁠Configuration

NOTE: It will be assumed that $PCAWG_DIR is /workflows/gitroot/pcawg_tools.

This workflow takes a few configuration options in its INI file:

workflow_id=12345
workflow_dir=/workflows/gitroot/pcawg_tools/pcawg_data.tasks
container_name=pancancer/pcawg_tools:0.0.1

• workflow_id - This is the ID of the workflow file you want to run in this particular instance of BroadWrapperWorkflow. This will be the name of a workflow file in jobs_dir.
• workflow_dir - This is the directory where workflow files will be generated. Normally, this is $PCAWG_DIR/pcawg_data.tasks but if you are generating workflow files like this:

scripts/pcawg_wf_gen.py gen --ref-download --create-service --work-dir <path_to_some_place_big>

then your INI file should have:

workflow_dir= <path_to_some_place_big>

• container_name - This is the name of the container to run. This should be set to pancancer/pcawg_tools:0.0.1.

⁠How to use

Ensure that the machine you are running this one has the docker images necessary for running Broad saved as tar files (docker_broad_variant_pipeline, docker_gatk, docker_genetorrent, docker_muse, galaxy) in the directory /workflows/gitroot/pcawg_tools.

You will also need to generate the pcawg_data.service file (using the script $PCAWG_DIR/scripts/pcawg_wf_gen.py) on this path:

/workflows/gitroot/pcawg_tools/pcawg_data.service

The pcawg_wf_gen.py can also be used to generate workflow files. You will need to generate some before running BroadWrapperWorkflow, as these workflow files will be passed by BroadWrapperWorkflow to the underlying Broad pipeline as input data.

You will also need to have the container pancancer/pcawg_tools. To build this container, follow these steps:

$ git clone https://github.com/ICGC-TCGA-PanCancer/pcawg_tools_container.git
$ cd pcawg_tools_container
$ docker build -t pancancer/pcawg_tools:0.0.1 .

Once everything is set up, you can run this workflow:

docker run --rm -it -h master -v /var/run/docker.sock:/var/run/docker.sock \
                          -v /datastore:/datastore \
                          -v /workflows:/workflows \
                          -v /workflows/gitroot/pcawg_tools/images:/workflows/gitroot/pcawg_tools/images:ro \
                          -v /workflows/gitroot/pcawg_tools/pcawg_data.service:/workflows/gitroot/pcawg_tools/pcawg_data.service:ro \
                          -v $(pwd)/broad_wrapper.ini:/workflow.ini \
           pancancer/seqware_whitestar_pancancer:1.1.1 \
                seqware bundle launch --dir /workflows/Workflow_Bundle_BroadWrapper_0.0.1-SNAPSHOT_SeqWare_1.1.1  --engine whitestar --no-metadata --ini /workflow.ini