If else for “temp” in snakemake
Let’s say I have a snakemake rule something like this
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 […]