cancerbits/pipes repository overview

⁠How to run pipelines for your project:

⁠Prerequisites:

• looper (http://looper.databio.org/en/latest/⁠) and pypiper (http://pypiper.databio.org/en/latest/⁠) need to be installed -- should already be available on all HPC servers
• clone this repo into your $CODEBASE:

cd $CODBASE
git clone [email protected]:cancerbits/pipes.git # or: git clone https://github.com/cancerbits/pipes.git

• the cancerbits/pipes docker image needs to be compiled and available (https://github.com/cancerbits/pipes/blob/master/containers/pipes.Dockerfile⁠) -- should already be available on all HPC servers

cd $CODEBASE/pipes/containers/
docker build -t cancerbits/pipes -f pipes.Dockerfile .

• your user must be a member of the docker group

⁠Project-specific configuration:

• generate a project config file. There's an example here: https://github.com/cancerbits/project_template/blob/main/metadata/config.yaml⁠
• generate a sample annotation table describing your samples. There's an example here: https://github.com/cancerbits/project_template/blob/main/metadata/samples.csv⁠
• mandatory columns include sample_name (no spaces, first symbol a letter), library (e.g. RNA-seq or ATAC-seq), organism (e.g. human), read_type (single-end or paired-end), and data_source (this specifies the pattern in config.yaml to be used to generate file paths)

⁠Execution:

looper run --sp SUBPROJECT_NAME metadata/config.yaml

Also useful looper rerun (if failed), looper check (check status), looper summarize (create summary tables)