Wrong argument type in log.debug
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bug
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- Nextflow
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Description
Description of the bug
Hi!
I think there's a very little bug in nf-core/tools.
At nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf, it should be:
debug(e.toString())
instead of
debug(e)
Command used and terminal output
Any pipeline with latest nf-core/tools would work.
The error I obtained can be reproduced on a system that does not have conda installed (at least not in the PATH).
nextflow run main.nf -profile conda,test
ERROR ~ Invalid method invocation `debug` with arguments: java.io.IOException: Cannot run program "conda": error=2, Aucun fichier ou dossier de ce nom (java.io.IOException) on Logger type
-- Check script 'subworkflows/nf-core/utils_nextflow_pipeline/main.nf' at line: 101 or see '.nextflow.log' file for more details
System information
Nextflow version: 25.04.8
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Research direction
Open nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf and inspect the logging call around lines 95-101. Reproduce the failure with nextflow run main.nf -profile conda,test on a system without conda, then verify that the error is logged without an invalid debug invocation.
Written by the indexing model from the issue text.
Assessment
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 1/5
- Estimated time
- Under an hour
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 45/100