config file taking it as literal string snakemake

  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.

you can move the information into the params section

rule test:
    input:
        xxxx
    params:
        ref=config['path']['ref_genome']
    output:
        xxxx
    shell:
        """
        cellranger-arc count --id={wildcards.atac_srr}_{wildcards.rna_srr} \
                                --reference={params.ref} \
                                --libraries=libraries/{wildcards.atac_srr}_{wildcards.rna_srr}_libraries.csv \
                                --localcores=48 \
                                --localmem=256
        """