This task aligns RNA-seq reads with HISAT2 using a metadata-driven workflow. Provide a fastq_folder (base for resolving relative paths), a TSV metadata with a Sample column plus either single-end (absolute-filepath) or paired-end (forward-absolute-filepath and reverse-absolute-filepath) columns, and a hisat2_index folder containing genome_index.*.ht2 files. For each row, reads are aligned (hisat2) and piped to samtools sort, producing /result/.bam.