I seem to be having trouble providing a correctly formatted bowtie2 index for parvovirus mapping. I've run bowtie2-build and generated the index and placed the files generated into a directory (references/ParvovirusB19/index). I'm pointing to this directory when running the pipeline, but I get this error: `WARN: Input tuple does not match input set cardinality declared by process

NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN

-- offending value: references/ParvovirusB19/index`

ERROR ~ Error executing process > 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (1)'

Caused by:

Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

My run command:

echo "Running viralrecon-nf"

${nextflow_exe} run ${module_dir}/main.nf \

--input ${sample_sheet} \

--outdir ${outdir} \

--platform illumina \

--protocol metagenomic \

-profile singularity \

--skip_asciigenome \

--fasta ${module_dir}/references/ParvovirusB19/ParvovirusB19.fasta \

--bowtie2_index ${module_dir}/references/ParvovirusB19/index/ \

-c ${viralrecon_config_file} \

--skip_pangolin \

--skip_kraken2 ${skip_kraken2} \

--skip_nextclade \

-with-report ${outdir}/${run_name}_report.html \

-resume

Hi there, This seems a fault on our side. Thanks for spotting this! Could you make an issue for this on the repository? You can rerun the analyis without providing ‘--bowtie2_index ${module_dir}/references/ParvovirusB19/index/ \’ and that issue will go away. Viralrecon will make a new index based the ‘—fasta’ file

Done! Thanks much! I was able to run it successfully without a user-supplied index.