DATASETS = ["PBMC_8K", "PBMC_4k"]

SALMON = "$BINS/salmon-0.14.0_linux_x86_64/bin/salmon"

rule all:
  input: expand("quants/{dataset}/alevin/quants_mat.gz", dataset=DATASETS)

rule salmon_quant:
    input:
        r1 = "reads/{sample}_1.fastq",
        r2 = "reads/{sample}_2.fastq",
		t2g = "$ANNO/txp2gene.tsv"
        index = "$INDICES/gencode.v29_salmon_0.14.0"
    output:
        "quants/{dataset}/alevin/quants_mat.gz"
    params:
        dir = "quants/{sample}"
    shell:
        "{SALMON} alevin -lISR --chromium -i {input.index} -p 8 -o {params.dir} -1 {input.r1} -2 {input.r2} --tgMap {t2g}"