ENCODE-DCC/atac-seq-pipeline: v2.2.0

Upgrade Caper to >=2.2.0 for new HPC features. $ pip install caper>=2.2.0 --upgrade Conda environment name change: encode-atac-seq-pipeline -> encd-atac Please reinstall your Conda environment after updating pipeline's git repo. $ scripts/uninstall_conda_env.sh $ scripts/install_conda_env.sh Caper's new HPC feature Unified command caper hpc for all HPC backend types (slurm, sge, pbs and lsf). Read Caper's README carefully and make a backup of your Caper's conf file (~/.caper/default.conf) and run caper init YOUR_BACKEND. caper hpc submit atac.wdl -i INPUT.json --leader-job-name GOOD_NAME_FOR_LEADER [--conda | --singularity]: submits a workflow to HPC's job engine. caper hpc list: shows all Caper leader jobs caper hpc abort JOB_ID: terminate a Caper leader job including child job