Is there an issue with the MULTIQC reporting and P...
# bacassm
Mark Pampuch
01/12/2025, 8:39 AMIs there an issue with the MULTIQC reporting and PROKKA for the BACASS pipeline? I ran a pipeline with 13 samples and got 13 annotated assemblies, but in the MULTIQC report I only get an annotation report for one of the assemblies (and I don’t even know which one)
d
Daniel_VM
01/14/2025, 8:35 AMHi @Mark Pampuch!, Which version of the pipeline are you using? Can you share the
nextflow runm
Mark Pampuch
01/14/2025, 10:56 AM Copy code
nextflow run nf-core/bacass -r 2.4.0 -c nextflow.config -profile singularity --input samplesheet.20241220.without.estimates.tsv --assembler dragonflye --assembly_type long --kraken2db /ibex/scratch/projects/c2303/20241221_KSA-lib-ONT-assemblies_canu_with-estimates/DATABASES/minikraken2_v2_8GB_201904.tgz --kmerfinderdb /ibex/scratch/projects/c2303/20241221_KSA-lib-ONT-assemblies_canu_with-estimates/DATABASES/bacteria.tar.gz --ncbi_assembly_metadata /ibex/scratch/projects/c2303/20241221_KSA-lib-ONT-assemblies_canu_with-estimates/ASSEMBLY-REPORTS/assembly_summary_refseq.txt --skip_kraken2 false --skip_kmerfinder false --outdir outputs/20250107_KSA-samples_dragonflye_without-sizes