name: "vsearch_cluster"
description: Cluster sequences using a single-pass, greedy centroid-based clustering algorithm.
keywords:
  - vsearch
  - clustering
  - microbiome
tools:
  - vsearch:
      description: VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
      homepage: https://github.com/torognes/vsearch
      documentation: https://github.com/torognes/vsearch/releases/download/v2.21.1/vsearch_manual.pdf
      tool_dev_url: https://github.com/torognes/vsearch
      doi: 10.7717/peerj.2584
      licence: ["GPL v3-or-later OR BSD-2-clause"]

input:
  - meta:
      type: map
      description: Groovy Map containing sample information e.g. [ id:'test' ]
  - fasta:
      type: file
      description: Sequences to cluster in FASTA format
      pattern: "*.{fasta,fa,fasta.gz,fa.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - aln:
      type: file
      description: Results in pairwise alignment format
      pattern: "*.aln.gz"
  - biom:
      type: file
      description: Results in an OTU table in the biom version 1.0 file format
      pattern: "*.biom.gz"
  - mothur:
      type: file
      description: Results in an OTU table in the mothur ’shared’ tab-separated plain text file format
      pattern: "*.mothur.tsv.gz"
  - otu:
      type: file
      description: Results in an OTU table in the classic tab-separated plain text format
      pattern: "*.otu.tsv.gz"
  - bam:
      type: file
      description: Results written in bam format
      pattern: "*.bam"
  - out:
      type: file
      description: Results in tab-separated output, columns defined by user
      pattern: "*.out.tsv.gz"
  - blast:
      type: file
      description: Tab delimited results in blast-like tabular format
      pattern: "*.blast.tsv.gz"
  - uc:
      type: file
      description: Tab delimited results in a uclust-like format with 10 columns
      pattern: "*.uc.gz"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@mirpedrol"
