rattle_snakefile

rule rattle_cluster:
        input:
                 "toyset/rna/input/sample.fastq"
        output:
                "toyset/rna/snakemake_output/clusters.out"
        shell:
                 """./rattle cluster -i {input} -t 24 -o toyset/rna/snakemake_output  --rna """

rule rattle_correct:
        input:
                clusters="toyset/rna/snakemake_output/clusters.out",
                fastq="toyset/rna/input/sample.fastq"
        output:
                "toyset/rna/snakemake_output/corrected.fq",
                "toyset/rna/snakemake_output/uncorrected.fq",
                "toyset/rna/snakemake_output/consensi.fq"

        shell:
                 """./rattle correct -i {input.fastq} -c {input.clusters} -o toyset/rna/snakemake_output -t 24  """

rule rattle_polish:
        input:
                "toyset/rna/snakemake_output/consensi.fq"
        output:
                "toyset/rna/snakemake_output/transcriptome.fq"
        shell:
                 """./rattle polish -i {input} -o toyset/rna/snakemake_output -t 24 --rna """