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
"""