prepare_spectra errors in stub mode because first() tries to get first item of empty directory
Open
Nobody has claimed this yet.
bug
- Dominant language
- Nextflow
- Stars
- 3
- Forks
- 1
- Avg merge
- 28m
- Merged PRs (30d)
- 1
Description
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
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Research direction
The issue identifies stub mode and the PREPARE_SPECTRA:THERMORAWFILEPARSER process, but names no file or test. Reproduce the shown workflow failure, then inspect the stub-mode path where first() reads an empty directory; done means the workflow completes successfully in stub mode.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100