RnaSnake/Includes/Quantification_Denovo.snake

Quantification_Dir = config["Quantification_Dir"]
SAMPLES_FILE = config["SAMPLES_FILE"]
TRINITY_HOME = config["TRINITY_HOME"]
transcripts = config["transcripts"]
gene_trans_map = config["gene_trans_map"]

rule rsem:
    input:
        config["Mapping_Dir"] + "/{sample}/bowtie2.bam"
    output:
        Quantification_Dir + "/{sample}.isoforms.results"
    threads: 4
    shell:
        "convert-sam-for-rsem {input} {input}.for_rsem;"
        "rsem-calculate-expression -p 8 --paired-end --bam --estimate-rspd --append-names"
        " {input}.for_rsem.bam {transcripts} {Quantification_Dir}/{wildcards.sample}"

rule merge_rsem:
    input:
        expand(Quantification_Dir + "/{sample}.isoforms.results", 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:
        "{TRINITY_HOME}/util/abundance_estimates_to_matrix.pl"
        " --est_method RSEM --gene_trans_map {gene_trans_map}"
        " --out_prefix {Quantification_Dir}/my {input};"