Unable to run ChIP-seq pipeline Docker container on HPC with Slurm (Error: "caper not found")

[eusoler]

Hello,

I am trying to run the ChIP-seq pipeline using the Docker container encodedcc/chip-seq-pipeline on an HPC system with Slurm. The environment I have access to uses Rocky Linux and Docker, and I am not able to install additional software.

Here is the command I am using to run the container:

docker run --rm -v "$WORK_DIR:/workspace" "encodedcc/chip-seq-pipeline:v2.2.2"
bash /opt/encode/pipelines/chip-seq.wdl
--json "/workspace/$(basename "$CONFIG_FILE")"
--out-dir "/workspace/salida_chipseq_$(basename "$CONFIG_FILE" .json)"

However, I am getting the following error:

docker: Error response from daemon: failed to create task for container: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "caper": executable file not found in $PATH: unknown.

It seems that the container is trying to run caper, but I don't have caper available in the environment, and I am unable to install it due to system restrictions.

My question is:

Is there any way to execute this pipeline without using caper? Or are there any recommended workarounds for running the pipeline in this environment?

Are there plans to create a version of the Docker container with caper pre-installed, or an alternative way to execute the pipeline directly from the Docker container?

Any help or suggestions would be greatly appreciated.

Thank you!