rule featureCounts:
    input:
        bam = config["Mapping_Dir"] + "/{sample}.bam",
        gtf = config["gtf"]
    output:
        readscount = config["Quantification_Dir"] + "/{sample}.count"
    threads: 6
    shell:
        "Rscript script/run-featurecounts.R -b {input.bam} -g {input.gtf} -o " +
        config["Quantification_Dir"] + "/{wildcards.sample}"

rule merge_featureCounts:
    input:
        readscounts = expand(config["Quantification_Dir"] + "/{sample}.count", sample = SAMPLES)
    output:
        gene_expr_matrix = config["Quantification_Dir"] + "/my.gene.TMM.EXPR.matrix",
        gene_counts_matrix = config["Quantification_Dir"] + "/my.gene.counts.matrix"
    shell:
        "perl script/abundance_estimates_to_matrix.pl --est_method featureCounts"
        " --out_prefix " + config["Quantification_Dir"] + "/my.gene"
        " {input.readscounts};"