shell:
    """
    cutadapt -a AGATCGGAAGAG -A AGATCGGAAGAG \
        -j {threads} \
        -o {output.cutadapt_r1} \
        -p {output.cutadapt_r2} \
        {input.r1} {input.r2} > {log} 2>&1
    """

shell:
    """
    fastqc -t {threads} {input.r1} {input.r2} \
        -o {params.out_dir} > {log} 2>&1
    """

shell:
    """
    featureCounts -T {threads} -p -t exon -g gene_name -a {params.gtf} \
        -o {output} {input} > {log} 2>&1
    """

shell:
    """
    hisat2 -p {threads} -N 1 --dta -x {params} \
        -1 {input.r1} \
        -2 {input.r2} \
        -S  {output}> {log} 2>&1
    """

shell:
    """
    samtools view {input} -q {threads} -h -S -b -o {output}> {log} 2>&1
    """

shell:
    """
    trimmomatic PE -threads {threads} -phred33 \
        {input.r1} \
        {input.r2} \
        {output.trim_r1} {output.trim_unpaired_r1} \
        {output.trim_r2} {output.trim_unpaired_r2} \
        LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:18 > {log} 2>&1
    """