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Thanks for testing it out. in comming fix here #168 . It is going to be available in in revision dev. It may take a bit longer to include it in the upcoming 2.4.0 release.
Note: I noticed you added param.ncbi_assembly_metadata along with skip_kmerfinder. However, the NCBI file is only used when the KmerFinder step is activated. Otherwise, the pipeline will not use the NCBI assembly metadata. (specifically, the kmerfinder module uses the info in the NCBI txt file to download candidate reference genome).
Ad Note ) That is residue from testing various options of the pipeline. Thanks for spotting it; I hope that it did not influence the pipeline performance. :)
Description of the bug
For some reson, canu is not running on ONT data (
GenomeSize
specified, reads provided withLongFastQ
,R1
,R2
andFast5
are set toNA
).Command used and terminal output
Relevant files
cano_not_executed.nextflow.log.zip
System information
running from interactive
bash
onUbuntu 22.04.4 LTS
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