Hi, I've been running a few other nf-core pipelines using Nextflow version 25.04.8, but I am having some trouble running even the test profile of rnavar. Does it require a newer version of Nextflow? Thanks. Here is the error I am running into: N E X T F L O W ~ version 25.04.8 Launching

<https://github.com/nf-core/rnavar>

[scruffy_goldberg] DSL2 - revision: 9db0282668 [master] Downloading plugin nf-core-utils@0.4.0 ERROR ~ Plugin nf-core-utils with version @0.4.0 does not exist in the repository

yes, it does require 25.10.2 at least

No problem! I got the test profile to run successfully, but when I try on real data I am running into this issue: Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_RNAVARPREPARE GENOMEGTF2BED (gencode.v44.primary_assembly.annotation.gtf)' Caused by: Process

NFCORE_RNAVAR:PREPARE_GENOME:GTF2BED (gencode.v44.primary_assembly.annotation.gtf)

terminated with an error exit status (127) Command executed: Rscript --no-save -<<'RCODE' gtf = read.table("gencode.v44.primary_assembly.annotation.gtf", sep=" ") gtf = subset(gtf, V3 == "exon") write.table(data.frame(chrom=gtf[,'V1'], start=gtf[,'V4'], end=gtf[,'V5']), "tmp.exome.bed", quote = F, sep=" ", col.names = F, row.names = F) RCODE awk '{print $1 " " ($2 - 1) " " $3}' tmp.exome.bed > exome.bed rm -rf tmp.exome.bed Command exit status: 127 Command output: (empty) Command error: .command.sh: line 2: Rscript: command not found Has anyone seen this before? For context, I am using Apptainer, and it has worked for other nf core pipelines so far.

Command not found usually means something went wrong with the container

Ah yes sorry about that. the directory where my cache was stored was full, so I moved it somewhere with more space and it worked. Thanks!

No worries, glad you solved it

Looking at the results now, my output says the pipeline completed successfully, but it appears that it stopped after BQSR, and didn't actually proceed to variant calling. Any tips here?

Could you share the log?

Hi sorry this was my mistake, I was only looking in the multiqc (in which I don't see qc of vcfs), but I do see the vcfs in the variant_calling folder of the output. My bad!

No problem