ERROR ~ 'com.fasterxml.jackson.core.io.ContentReference com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(java.lang.Object)'

[georgiesamaha]

Description of the bug

Running 3.12.0 with Nextflow Tower triggers an error also observed with rnafusion workflow.

Command used and terminal output

nextflow run https://github.com/nf-core/rnaseq \
		 -name admiring_rubens \
		 -params-file https://tower.services.biocommons.org.au/api/ephemeral/WqSfsU4_Hk4HlOWt5X52Lg.json \
		 -with-tower https://tower.services.biocommons.org.au/api \
		 -r 3.12.0 \
		 -profile nci_gadi,singularity,test

Relevant files

nf-3usco1CoAgiMmR.log

System information

• Nextflow version: Nextflow/23.04.3
• Hardware: NCI Gadi HPC
• Executor: PBSpro
• Container engine: Singularity
• OS: Rocky linux 8
• nf-core/rnaseq version: 3.12.0

[MatthiasZepper]

This is a problem with Nextflows Tower plugin and its dependencies and not with the nf-core rnaseq pipeline. Please contact Seqera's support instead.

(Maybe using the nextflow-all binaries could help.)

[georgiesamaha]

Thanks Matthias, will chase that up