Is this compatible with apptainer? My HPC recently switched to apptainer over from singularity and I keep getting this error:

Caused by:
  Process `NFCORE_METATDENOVO:METATDENOVO:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)` terminated with an error exit status (127)


Command executed:

  check_samplesheet.py \
      samplesheet.csv \
      samplesheet.valid.csv
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METATDENOVO:METATDENOVO:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

Command error:
  env: 'apptainer': No such file or directory

Work dir:
  /scratch1/zjhennin/metatranscript/fa/80554cd85bdc31b3d723662270b744

Container:
  /scratch1/zjhennin/metatranscript/singularity/quay.io-biocontainers-python-3.8.3.img

AFAIK, that should work out of the (Nextflow) box and is not something pipeline specific. To me, your error message looks like Nextflow couldn't find the

apptainer

program. Is there a module you need to load or something? Is the executable on your

PATH

(run

which apptainer

)?

Okay thanks! I’ve let my admins know