ERROR ~ Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)'

[tbooth]

Description of the bug

Error trying to run the workflow in test mode when using singularity.

Command used and terminal output

$ nextflow run nf-core/chipseq -profile test,singularity --outdir .

...

Execution cancelled -- Finishing pending tasks before exit
-[nf-core/chipseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_CHIPSEQ:PREPARE_GENOME:GTF2BED (genes.gtf)'

Caused by:
  Process `NFCORE_CHIPSEQ:PREPARE_GENOME:GTF2BED (genes.gtf)` terminated with an error exit status (255)


Command executed:

  gtf2bed \
      genes.gtf \
      > genes.bed
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CHIPSEQ:PREPARE_GENOME:GTF2BED":
      perl: $(echo $(perl --version 2>&1) | sed 's/.*v\(.*\)) built.*/\1/')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  WARNING: Skipping mount /mnt/lustre/e1000/home/edg01/edg01/shared/software/singularity/conda-env/envs/singularity/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  INFO:    Cleaning up image...
  FATAL:   container creation failed: mount /tmp/nextflow_test/work->/tmp/nextflow_test/work error: while mounting /tmp/nextflow_test/work: destination /tmp/nextflow_test/work doesn't exist in container

Work dir:
  /tmp/nextflow_test/work/19/ff6617324984e5332e850ee712dc96

Container:
  /tmp/nextflow_test/work/singularity/depot.galaxyproject.org-singularity-perl-5.26.2.img

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details

Relevant files

No response

System information

N E X T F L O W version 25.04.3 build 5949 Running on HPC, local executor singularity version 3.8.6 Red Hat Enterprise Linux release 8.1 (Ootpa) x86_64 GNU/Linux

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  nf-core/chipseq v2.1.0-g76e2382
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : gigantic_murdock
  containerEngine           : singularity
  launchDir                 : /tmp/nextflow_test
  workDir                   : /tmp/nextflow_test/work
  projectDir                : /home/edg01/edg01/tbooth2/.nextflow/assets/nf-core/chipseq
  userName                  : tbooth2
  profile                   : test,singularity
  configFiles               : 

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/samplesheet/v2.1/samplesheet_test.csv
  read_length               : 50
  outdir                    : .

Reference genome options
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa
  gtf                       : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf

Process skipping options
  skip_preseq               : true

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

Generic options
  fingerprint_bins          : 100