David Carlson
05/14/2025, 12:32 PMdev version of the pipeline for the first time and I noticed that the pipeline will fail immediately with the following error if the absolute path to the ONT reads is not provided in the sample sheet:
May-14 08:23:39.293 [Actor Thread 92] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_GENOMEASSEMBLER:GENOMEASSEMBLER:ONT:JELLYFISH:COUNT (1); work-dir=null
error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value: './ONT_data_combined.fastq.gz'
May-14 08:23:39.294 [Actor Thread 93] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_GENOMEASSEMBLER:GENOMEASSEMBLER:ONT:PREPARE_ONT:RUN_NANOQ:NANOQ (1); work-dir=null
error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value: './ONT_data_combined.fastq.gz'
May-14 08:23:39.303 [Actor Thread 76] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_GENOMEASSEMBLER:GENOMEASSEMBLER:ONT:JELLYFISH:COUNT; work-dir=null
error [java.lang.InterruptedException]: java.lang.InterruptedException
May-14 08:23:39.311 [Actor Thread 93] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot get property 'containerEngine' on null object
Providing the absolute path (relative paths do not work) avoids this error. This doesn't appear to stated in the documentation. Is this requirement for the absolute path to the reads expected behavior?