Snakefile_cellranger

from os.path import join
configfile: "config_cellranger.yaml"

cellranger=config["CELLRANGER"]
thread=config["THREAD"]
outprefix=config["OUTPUT"]
index=config["INDEX"]
fastqs=config["FASTQS"]
sample=config["SAMPLE"]

rule all:
    input: expand("cellranger_out/{outprefix}_out/outs/metrics_summary.csv", outprefix=config["OUTPUT"])

rule run_cellranger:
    output:
        "cellranger_out/{outprefix}_out/outs/metrics_summary.csv"
    benchmark:
        "benchmarks_cellranger/{outprefix}.txt"
    shell:
        """
         rm -rf cellranger_out/{outprefix}_out
         cd cellranger_out
         {cellranger} count --id={outprefix}_out --transcriptome={index} --fastqs=../{fastqs} --localcores={thread} --sample={sample} --nosecondary
         cd ..
        """