Unable to override container entrypoint in kubernetes with fusion and wave enabled

[oqadiSAK]

Bug report

We are aware that Nextflow expects images to have /bin/bash ENTRYPOINT by definition. But we are able to override our images entrypoint to fit /bin/bash in local executor environment. Can't achieve this in k8s executor.

Expected behavior and actual behavior

Container entrypoint should be configurable when using Nextflow with k8s, Fusion, and Wave configurations.
Currently, all attempted methods to override container entrypoint fail in this environment combination.

Steps to reproduce the problem

1. Create a simple Nextflow setup with Fusion and Wave:

wave {
    enabled = true
    endpoint = '${WAVE_URL}'
}

fusion {
    enabled = true
}

workDir = '${S3_WORKDIR}'

k8s {
    namespace = 'nextflow'
    serviceAccount = 'nextflow-sa'
}

process test_process {
    container '${CONTAINER}'
    script:
    """
    echo "hello"
    """
}

workflow {
    test_process()
}

2. Attempted override methods (all failed):

# Method 1: Process containerOptions
process {
    containerOptions '--entrypoint=""'
}

# Method 2: Configuration settings
k8s {
    entrypointOverride = true
}

docker {
    entrypointOverride = true
}

process {
    entrypointOverride = true
}

# Method 3: Environment variable
export NXF_CONTAINER_ENTRYPOINT_OVERRIDE=true

Reference: Entrypoint override implementation in source code:

nextflow/modules/nextflow/src/main/groovy/nextflow/k8s/K8sConfig.groovy

Line 140 in 62263a3

boolean entrypointOverride() {

Program output

No error messages are shown - the entrypoint override simply does not take effect when using k8s, Fusion, and Wave together.

Environment

• Nextflow version: 24.10.4 build 5934
• Java version: openjdk 21-internal 2023-09-19
• Operating system: Ubuntu 24.04
• Bash version: 5.1.16(1)-release (x86_64-pc-linux-gnu)

Additional context

• The entrypoint override works correctly with local executor using containerOptions in the process definition
• We need this functionality to run containers that have entrypoints different from /bin/bash
• There is no clear documentation for entrypoint override configuration in k8s