Snakefile

rule download_data:
    output:
        reads="raw_data/sample1.fastq.gz"
    shell:
        """
        mkdir -p raw_data
        cd raw_data
        wget https://raw.githubusercontent.com/deto/Snakemake_Tutorial/master/misc/sample1.fastq.gz
        """

rule fastqc:
    input:
        reads=rules.download_data.output
    output:
        "fastqc/results.html"
    shell:
        """
        fastqc --outdir="fastqc" {input.reads}
        """

rule align_reads:
    input:
        reads=rules.download_data.output
    output:
        "STAR/results.bam"
    shell:
        """
        STAR --genomeDir "/some/directory/to/reference" \
            --outFileNamePrefix "STAR/results" \
            --readFilesIn {input.reads}
        """

rule quantify_transcripts:
    input:
        bam=rules.align_reads.output
    output:
        isoforms="rsem/sample.isoforms.results"
    shell:
        """
        rsem-calculate-expression --alignments {input.bam} rsem/sample
        """

rule plot_results:
    input:
        isoforms=rules.quantify_transcripts.output.isoforms
    output:
        plot="plots/my_plot.png"
    script: "scripts/plot_things.py"

rule all:
    input:
        rules.plot_results.output,
        rules.fastqc.output,