prepare_spectra errors in stub mode because first() tries to get first item of empty directory

[svenbioinf]

Description of the bug

see element for possible fix

Command used and terminal output

Assertion failed: 
  
  assert workflow.success
         |        |
         workflow false
  
  Nextflow stdout:
  
  ERROR ~ Error executing process > 'PREPARE_SPECTRA:THERMORAWFILEPARSER (2)'
  
  Caused by:
    Process `PREPARE_SPECTRA:THERMORAWFILEPARSER (2)` terminated with an error exit status (1)
  
  
  Command executed:
  
    ThermoRawFileParser.sh \
        -i sample2.raw \
        -b 2.mzML \
        --format 2
  
  Command exit status:
    1
  
  Command output:
    2026-04-17 11:35:29 INFO Started parsing sample2.raw
    2026-04-17 11:35:29 ERROR Unable to access the RAW file using the native Thermo library.

Relevant files

No response

System information

No response