shell:
    """
    cellranger-arc count --id={wildcards.atac_srr}_{wildcards.rna_srr} 
                         --reference={config['path']['ref_genome']} 
                         --libraries=libraries/{wildcards.atac_srr}_{wildcards.rna_srr}_libraries.csv 
                         --localcores=48 
                         --localmem=256
    """

Hi all, just wanted to ask, for the reference flag, I have a config file that has the path to the reference genome, but snakemake seems to read it as string instead of reading the variable in the config file.

I tried removing the curly braces too and it doesn’t work.