name: graphmap2_align description: A versatile pairwise aligner for genomic and spliced nucleotide sequences keywords: - align - fasta - fastq - genome - reference tools: - graphmap2: description: | A versatile pairwise aligner for genomic and spliced nucleotide sequences. homepage: https://github.com/lbcb-sci/graphmap2 documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fastq: type: file description: | List of input FASTQ files and paired-end data, respectively. - fasta: type: file description: | Reference database in FASTA format. - index: type: file description: | FASTA index in gmidx. output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - sam: type: file description: Alignment in SAM format pattern: "*.sam" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh"