container creation failed while running on test data and singularity

[GuidoBarzaghi]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/rnaseq pipeline documentation

Description of the bug

Hello! Similarly to #494, I have been having issues running the rnaseq pipeline on the test dataset using singularity. Up to now, I've been playing around with various versions of both the rnaseq pipeline, nextflow, singularity and even squashfs-tools. Nothing seems to help though.

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run nf-core/rnaseq -r 3.4 -profile test,singularity
2. See error: FATAL: container creation failed: mount /proc/self/fd/13->/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/13: kernel reported a bad superblock for squashfs image partition, possible causes are that your kernel doesn't support the compression algorithm or the image is corrupted

Expected behaviour

I would expect the pipeline to create the container and allow for the job to be run

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline
• The nextflow.log file

System

• Hardware: HPC
• Executor: slurm
• OS: CentOS Linux
• Version 7.6.1810

Nextflow Installation

• Version: 21.04.3 build 5560

Container engine

• Engine: Singularity
• version: 3.9.0-rc.1

Additional context

[GuidoBarzaghi]

Assigning fresh folders to the following solved the issue

• SINGULARITY_CACHEDIR
• SINGULARITY_TMPDIR
• NXF_SINGULARITY_CACHEDIR
• NXF_HOME