Snakefile

PRE = "transcripts"
GTF = "{0}.gtf.gz".format(PRE)
FASTA = "{0}.fasta.gz".format(PRE)
INDEX = "{0}.kidx".format(PRE)

rule all:
    input:
        "quant_out/abundance.tsv",
        "bus_out/output.bus"

rule index:
    input: FASTA
    output: INDEX
    shell:
        """
        kallisto index -i {output} {input}

        mkdir quant_out
        mkdir bus_out
        """

rule kallisto_quant:
    input:
        "reads_1.fastq.gz",
        "reads_2.fastq.gz",
        INDEX
    output:
        "quant_out/abundance.tsv",
        "quant_out/run_info.json"
    shell:
        """
        kallisto quant \
        -i {INDEX} \
        -b 30 \
        -o quant_out/ \
        --genomebam \
        --gtf {GTF} \
        --chromosomes chrom.txt \
        {input[0]} {input[1]}
        """

rule kallisto_bus:
    input:
        "sc_reads_1.fastq.gz",
        "sc_reads_2.fastq.gz",
        INDEX
    output:
        "bus_out/matrix.ec",
        "bus_out/transcripts.txt",
        "bus_out/output.bus",
        "bus_out/run_info.json"
    shell:
        """
        kallisto bus \
        -i {INDEX} \
        -x 10xv2 \
        -o bus_out \
        -t 4 \
        {input[0]} {input[1]}
        """