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Description
Returns an error when I used with "ask_merlin" parameter, but will successfully run the pipeline without "ask_merlin"
Steps to Reproduce
bactopia --samples "$dataset/${dataset}_samples.txt"
-profile docker
--shovill_assembler spades
--species Staphylococcus aureus
--genome_size 2800000
--coverage 100
--max_cpus 8
--ask_merlin
--outdir "$dataset/output"
--cleanup_workdir
-resume
ERROR ~ No such variable: Exception evaluating property 'fastq_only' for nextflow.script.ChannelOut, Reason: groovy.lang.MissingPropertyException: No such property: fastq_only for class: groovyx.gpars.dataflow.DataflowBroadcast
-- Check script '/opt/mamba/envs/bactopia/share/bactopia-3.2.0/./workflows/bactopia.nf' at line: 78 or see '.nextflow.log' file for more details
Execution Environment
- Bactopia Version: 3.2
- OS: Ubuntu
- Environment: conda
Additional Information
Any other information you think might be helpful in squashing this bug.