nextflow-io / nextflow-io/nextflow

Google Batch: Setting `accelerator` directive removes docker ENTRYPOINT instructions

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executor/google-batch software/docker triage/investigate
Dominant language
Groovy
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Description

Bug report

As the title says, if somebody provides "accelerator" to the configuration of a process, the container of that process does not start with the pre-defined entrypoint from the dockerfile it was built from.

A "minimal" example:

entrypoint.sh:

echo "hello world"
bash $@

Dockerfile:

FROM python:3.13-slim 
# Setting up home
ENV HOME=/home/root
WORKDIR /home/root
RUN chmod 777 /home/root
COPY entrypoint.sh /home/root/entrypoint.sh
ENTRYPOINT ["/home/root/entrypoint.sh"]

Build the container and push it to Artifact Registry, say to CONTAINER_URI

example.nf:

processAc {
   container: CONTAINER_URI
   accelerator: [limit: 1, type: 'nvidia-tesla-t4']
   script:
   """
   exit 0
   """
}

processWoAc {
   container: CONTAINER_URI
   script:
   """
   exit 0
   """
}

workflow {
processAc()
processWoAc()
}

The google batch logs of processWoAc task will show the "hello world" message, but not for processAc task.

Environment
  • Nextflow version: 26.04.4

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce the behavior using entrypoint.sh, the Dockerfile, and example.nf, then compare the Google Batch logs for processAc and processWoAc. Trace how the accelerator setting changes container startup; done means the accelerator task also runs the Dockerfile ENTRYPOINT and prints the expected "hello world" message.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, google-cloud
Domain
cloud, devops
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
48/100

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