Hi! I am trying to use the new version of Sarek (v 3.7.1) to perform BBsplit on some PDXs samples. I have created the file (csv) containing the fasta reference of the mouse genome as follows: mm10,/path/genome_mm10_def.fa However, the following error keeps appearing while running it: -[nf-core/sarek] Pipeline completed with errors- WARN: Killing running tasks (4) ERROR ~ Error executing process > 'NFCORE_SAREKPREPARE GENOMEBBMAP_BBSPLIT (build_index)' Caused by: Cannot invoke method getName() on null object it looks like its not able to retreive my mouse reference file (which is in an available folder with permissions). This is the script I have created to launch sarek: nextflow run $pipeline \ -profile $profile \ -r $version \ --input $samples \ --outdir $outdir \ --tools $tools \ --bbsplit_fasta_list ref_bbsplit.csv \ --genome $genome \ --pon $pon \ --multiqc_title "PDX_report" \ -c $config \ --wes \ --pon_tbi $pon_index \ --intervals "$intervals" I was wondering if anyone has encountered the same error, as I am not sure how to fix it. Thanks!

can you share the nextflow version and the relevant log please?

Hi Rike, I have realised which was the mistake, as I did not add as inout the required index folder for bbsplit. Thanks!