name: megahit description: An ultra-fast metagenomic assembler for large and complex metagenomics keywords: - megahit - denovo - assembly - debruijn - metagenomics tools: - megahit: description: "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph" homepage: https://github.com/voutcn/megahit documentation: https://github.com/voutcn/megahit tool_dev_url: https://github.com/voutcn/megahit doi: "10.1093/bioinformatics/btv033" licence: ['GPL v3'] input: - meta: type: map description: | Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed) 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 in gzipped or uncompressed FASTQ or FASTA format. 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" - contigs: type: file description: Final final contigs result of the assembly in FASTA format. pattern: "*.contigs.fa.gz" - k_contigs: type: file description: Contigs assembled from the de Bruijn graph of order-K pattern: "k*.contigs.fa.gz" - addi_contigs: type: file description: Contigs assembled after iteratively removing local low coverage unitigs in the de Bruijn graph of order-K pattern: "k*.addi.fa.gz" - local_contigs: type: file description: Contigs of the locally assembled contigs for k=K pattern: "k*.local.fa.gz" - kfinal_contigs: type: file description: Stand-alone contigs for k=K; if local assembly is turned on, the file will be empty pattern: "k*.final.contigs.fa.gz" authors: - "@jfy133"