unixbioinformaticssnakemake

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.


Solution

  • 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
            """