shell:
    """
    mkdir -p {params.outfolder}
    fastqc {input.fastq1} {input.fastq2} -o {params.outfolder}
    """    

shell: 
    """
    fastp -i {input.fastq1} -I {input.fastq2} -o {output.trimmed_fastq_R1} -O {output.trimmed_fastq_R2} -h trimmed_fastq/{wildcards.fastq}_fastp.html -j trimmed_fastq/{wildcards.fastq}_fastp.json
    """

shell: 
    """
    STAR --runMode alignReads \
    --genomeDir {params.genome_dir} \
    --readFilesIn {input.trimmed_fastq_R1} {input.trimmed_fastq_R2} \
    --readFilesCommand zcat \
    --outSAMtype BAM SortedByCoordinate \
    --outFileNamePrefix {params.prefix}
    """

shell:
    """
    featureCounts -a {params.GTF} \
    -o {output.counts} \
     {input.bam_files}
    """

shell:
    """
    multiqc \
        --dirs {params.fastqc_dir} {params.fastp_dir} {params.bam_dir} {params.subreads_dir}
    """