Issue with symbolic links on 10XGENOMICS preprocessing workflow

[AdrianParrilla]

Hi!

I was trying to run the pipeline using a SMB-mounted directory in a network cluster, but I got an error at the beginning regarding symbolic links:

"Command error: ln: failed to create symbolic link 'samplesheet_ATAC.csv': Operation not supported"

The pipeline was under the /mnt/smb/TDA directory and the input command with a custom genome was:

nextflow run main.nf -profile docker --preprocess 10xgenomics --outdir /mnt/smb/TDA/scATAC_files/results --input_fastq /mnt/smb/TDA/scATAC_files/samplesheet_ATAC.csv --ref_fasta /mnt/smb/TDA/scATAC_files/masked_genome.fa --ref_gtf /mnt/smb/TDA/scATAC_files/Homo_sapiens.GRCh38.112.gtf --species_latin_name 'homo sapiens'

Attached you'll find the .nextflow.log file I got: nextflow.log

Do I have to change any additional configuration of the pipeline?

Thanks in advance for you help,

Best,

Adrian