name: miniasm description: A very fast OLC-based de novo assembler for noisy long reads keywords: - assembly - pacbio - nanopore tools: - miniasm: description: Ultrafast de novo assembly for long noisy reads (though having no consensus step) homepage: https://github.com/lh3/miniasm documentation: https://github.com/lh3/miniasm tool_dev_url: https://github.com/lh3/miniasm doi: "10.1093/bioinformatics/btw152" 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 PacBio/ONT FastQ files. pattern: "*.{fastq,fastq.gz,fq,fq.gz}" - paf: type: file description: Alignment in PAF format pattern: "*{.paf,.paf.gz}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - gfa: type: file description: Assembly graph pattern: "*.gfa.gz" - assembly: type: file description: Genome assembly pattern: "*.fasta.gz" authors: - "@avantonder"