Hello! I ran the pipeline successfully on three test samples with following parameters: nextflow run nf-core/circrna -r dev \ -profile singularity \ -w circ_RNA_seq_test_2/work \ --input samplesheet_test.csv \ --outdir circ_RNA_seq_test_2/results \ --genome GRCh38 \ --tools circexplorer2,ciri,find_circ \ --min_tools 2 \ --save_intermediates \ --bsj_reads 2 \ --mirna_tools miranda,targetscan \ --mirna_min_tools 2 \ -resume I noticed that the work directory is very large with more than 800GB. I need to run this on 53 samples, which will most likely hit the limit of my scratch quota. As I understand, the --save-intermediates just influences the result directory and not the work directory. The biggest files are the different sam files produced by different tools. Is there a way to reduce this memory footprint? Thank you for your help in advance!

Hey, nice to hear you had a good experience with the pipeline! You might want to check out the nf-boost plugin, that automatically deletes intermediate directories that will not be needed anymore while the pipeline is still running. I hope this fixes it for you. Let me know how it goes!

Thank you, I will give it a try.