Running Nextflow inside a Docker container.

[hjn0415a]

Bug report

I'm trying to run Nextflow inside a Docker container.
After building the Docker image, I ran a Nextflow command inside the container,
But I encountered the following error message:

bash: .command.run: No such file or directory

The error says .command.run: No such file, but the file does exist in the work directory inside the container. However, when I run the command bash .command.run from that work directory, I still get the same error.

Here is the Dockerfile I used:
Dockerfile.txt

(Please follow this template by replacing the text between parentheses with the requested information)

Steps to reproduce the problem

1. Build the Dockerfile I've attached with the following command:
   docker build -t quantms-base .

2. Start the container with the following command:

docker run -it --rm --privileged `
  -v /var/run/docker.sock:/var/run/docker.sock `
  -v ${pwd}:/workspace `
  quantms-base bash

3. Move to the /workspace directory, then run the following command:
   nextflow run bigbio/quantms -r dev -profile docker,test_lfq

(Provide a test case that reproduces the problem either with a self-contained script or GitHub repository)

Program output

Command error:
  bash: .command.run: No such file or directory

Work dir:
  /workspace/work/68/293efb718638d400aaa49a52c67662

.nextflow.log

(Copy and paste the output produced by the failing execution. Please highlight it as a code block. Whenever possible upload the .nextflow.log file.)

Environment

• Nextflow version: [25.04.4]
• Java version: [17.0.10]
• Operating system: [macOS, Linux, etc] Linux Ubuntu
• Bash version: (use the command $SHELL --version) 5.1.16(1)-release (x86_64-pc-linux-gnu)