Nextflow docker permission issues

[ivansg44]

From the README:

One currently unresolved issue: If you upload a file while the application is deployed through Docker, and then later attempt to upload a file while the application is deployed locally, the application will likely run into permission issues related to the nf-ncov-voc cache. You can fix this by removing all cache files in the nf-ncov-voc/ directory:

$ rm -r results work .nextflow .nextflow.log* capsule framework plugins secrets tmp

You may have to use sudo.

[ivansg44]

@anwarMZ found this:

Running Nextflow using a Docker-in-Docker approach can indeed lead to permission issues, especially with files and directories that are shared between the host and the containers. Let's address this issue specifically for a Docker-in-Docker setup:
Docker-in-Docker Volume Mounting: Ensure that the .nextflow directory is properly mounted into the outer Docker container. You might need to add a volume mount for this directory.
Permissions in Docker: The user inside the Docker container might not have the same UID as your host user, leading to permission issues.
Workaround using NXF_HOME: Set the NXF_HOME environment variable to a directory that is definitely writable within the Docker container.
Here are some steps to try:
Modify your Docker run command to include a volume mount for the Nextflow home directory:
docker run -v /path/on/host/.nextflow:/root/.nextflow ...
Inside your Docker container, set the NXF_HOME environment variable to a known writable location:
export NXF_HOME=/tmp/nextflow
mkdir -p $NXF_HOME
chmod 777 $NXF_HOME
If you're using a Docker Compose file, you can add these environment variables and volumes there:
version: '3'
services:
nextflow:
image: your-nextflow-image
environment:
- NXF_HOME=/tmp/nextflow
volumes:
- /path/on/host/.nextflow:/tmp/nextflow
If you're running Nextflow from within a script inside the Docker container, you can set the NXF_HOME at the beginning of the script:
#!/bin/bash
export NXF_HOME=/tmp/nextflow
mkdir -p $NXF_HOME
chmod 777 $NXF_HOME
nextflow run ...
Ensure that the user running Nextflow inside the Docker container has write permissions to the directory specified by NXF_HOME.
After making these changes, try running your Nextflow pipeline again.
If you're still encountering issues, please provide:
Your Docker run command or Docker Compose file
The Dockerfile you're using for your Nextflow image
The exact error message you're seeing
The output of ls -la $NXF_HOME from inside the Docker container
This additional information will help us further diagnose and resolve the permission issue in your Docker-in-Docker setup.