name: hisat2_align description: Align RNA-Seq reads to a reference with HISAT2 keywords: - align - fasta - genome - reference tools: - hisat2: description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ['MIT'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - index: type: file description: HISAT2 genome index file pattern: "*.ht2" - splicesites: type: file description: Splices sites in gtf file pattern: "*.{txt}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - summary: type: file description: Aligment log pattern: "*.log" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@ntoda03"