With the most recent updates on the dev branch, it seems the ciriquant + Hisat2 index building problem is fixed. However I ran into a downstream problem. Here is the error message: Jul-23 105626.634 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > ‘NFCORE_CIRCRNACIRCRNAQUANTIFICATION:JOIN_GENE_COUNTS (gene_counts)’ Caused by: Process

NFCORE_CIRCRNA:CIRCRNA:QUANTIFICATION:JOIN_GENE_COUNTS (gene_counts)

terminated with an error exit status (255) Command executed: csvtk \ join \ -f 1,2 -t \ --num-cpus 1 \ --out-file gene_counts.csv \ PDX5.gene_counts.tsv cat <<-END_VERSIONS > versions.yml “NFCORE_CIRCRNACIRCRNAQUANTIFICATIONJOIN GENE COUNTS” csvtk: $(echo $( csvtk version | sed -e “s/csvtk v//g” )) END_VERSIONS Command exit status: 255 Command output: (empty) Command error: [ERRO] two or more files needed

What does your samplesheet look like? Are you trying to analyze only a single sample?

Indeed, there was only one sample in the samplesheet. After adding another one, it ran through. 🥳

Good to hear. Processing a single sample is an edge case that I have not yet thought about. But I guess there will not be any real-world example for this, cause in most experimental designs you will have at least two conditions and/or multiple replicates. So my preferred way would be to throw an error whenever only a single sample is provided, because implementing proper handling is not straightforward and most likely not worth it

Re: the ciriquant/hisat problem, indeed it is not stable yet. On a test sample, it failed on the first try, but went through on a second try.