Singularity parameters --home and --bind set by default but disallowed on HPC cluster

[matmu]

Version

I am using the following versions on our HPC cluster:
Snakemake c5.4.4
singularity version 3.5.3

Minimal example

singularity: "docker://bash"

rule test:
    shell: "echo test"

Describe the bug

snakemake --use-singularity --debug

returns this message:

Building DAG of jobs...
Pulling singularity image docker://bash.
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	test
	1

[Fri Mar 13 15:59:30 2020]
rule test:
    jobid: 0

Activating singularity image /data/nanopore/test/.snakemake/singularity/36b22e49e8a03fd08160e9345dd1034e.simg
FATAL:   container creation failed: not mounting user requested home: user bind control is disallowed
[Fri Mar 13 15:59:30 2020]
Error in rule test:
    jobid: 0

RuleException:
CalledProcessError in line 4 of /data/nanopore/test/Snakefile:
Command ' singularity exec --home /data/nanopore/test  --bind /opt/snakemake/v5.4.4/lib/python3.5/site-packages/snakemake-5.4.4-py3.5.egg:/mnt/snakemake /data/nanopore/test/.snakemake/singularity/36b22e49e8a03fd08160e9345dd1034e.simg bash -c 'set -euo pipefail;  echo test'' returned non-zero exit status 255
  File "/data/nanopore/test/Snakefile", line 4, in __rule_test
  File "/usr/lib/python3.5/concurrent/futures/thread.py", line 55, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /data/nanopore/test/.snakemake/log/2020-03-13T155917.601627.snakemake.log

Apparently, snakemake runs singularity with default values for --home and --bind. These were disallowed by the administrator, however.

Executing

singularity exec --home /data/nanopore/test  --bind /opt/snakemake/v5.4.4/lib/python3.5/site-packages/snakemake-5.4.4-py3.5.egg:/mnt/snakemake /data/nanopore/test/.snakemake/singularity/36b22e49e8a03fd08160e9345dd1034e.simg bash -c 'set -euo pipefail;'

returns:

FATAL:   container creation failed: not mounting user requested home: user bind control is disallowed

Additional context
Is there a way to disable the Singularity default parameter setting in snakemake? Inside the singularity container the /data directory is still writeable and readable anyway.

Thanks a lot

[frankier]

This might help: #1206

[Saranya-Balachandran]

Was this fixed?