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"Path value cannot be null" error during featurelinkerunlabeledkd step #87

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plashmore opened this issue Mar 20, 2024 · 1 comment
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Description of the bug

During workflow with peakpickerhires->featurefindermetabo->mapalignerposecluster->maprttransformer workflow stops after mapalignerposecluster step with error "Error executing process Caused by: Path value cannot be null"

Previously had to make adjustment to the modules.config file to get the peakpickerhires step to work (added .centroided to the filename.mzML in line 48) and had to adjust paths on lines 137 and 175 to remove ${meta.id} to fix "filename too long" error.

Command used and terminal output

command: nextflow run nf-core/metaboigniter -profile docker

output: 
WARN: Input tuple does not match input set cardinality declared by process `NFCORE_METABOIGNITER:METABOIGNITER:LINKER:OPENMS_FEATURELINKERUNLABELEDKD` -- offending value: [id:Linked_data]
ERROR ~ Error executing process > 'NFCORE_METABOIGNITER:METABOIGNITER:LINKER:OPENMS_FEATURELINKERUNLABELEDKD (1)'

Caused by:
  Path value cannot be null

Relevant files

files.zip

System information

Nextflow version: 23.10.1
Metaboigniter version: 2.0.0
Hardware: Desktop
Executor: local
Container engine: Docker
OS: Linux (Fedora 39)

@plashmore plashmore added the bug Something isn't working label Mar 20, 2024
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plashmore commented Mar 21, 2024

this was related to the centroided data error, applying the appropriate fixes to fix the centroiding issue makes this error moot

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