unexpected module behaviour

[fredjaya]

There appears to be a problem with the module-installed nextflow and singularity binaries. When loaded via modules, they are visible in PATH but fail to run with sudo, and for nextflow, without. Running the full path with sudo works, which suggests a permissions or environment issue with the module setup.

Environment

Nectar with bioimage_rstudio.

Steps to reproduce

Load nextflow module and attempt to run:

module load nextflow
nextflow

Output:

mkdir: cannot create directory ‘/apps/nextflow/24.10.2/framework/25.10.4’: Permission denied

whereis nextflow
nextflow: /apps/nextflow/24.10.2/bin/nextflow

which nextflow
/apps/nextflow/24.10.2/bin/nextflow

Direct execution:

/apps/nextflow/24.10.2/bin/nextflow

Same error:

mkdir: cannot create directory ‘/apps/nextflow/24.10.2/framework/25.10.4’: Permission denied

Running with sudo and the full path works:

sudo /apps/nextflow/24.10.2/bin/nextflow

A similar thing happens with singularity too.

module load singularity
singularity # this works fine

But sudo doesn't work

sudo singularity
sudo: singularity: command not found

Running with full path is ok

which singularity
/opt/singularity/4.2.1/bin/singularity

sudo singularity
sudo: singularity: command not found