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meta.yml
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meta.yml
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name: gtdbtk_classifywf
description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.
keywords:
- GTDB taxonomy
- taxonomic classification
- metagenomics
- classification
- genome taxonomy database
- bacteria
- archaea
tools:
- gtdbtk:
description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.
homepage: https://ecogenomics.github.io/GTDBTk/
documentation: https://ecogenomics.github.io/GTDBTk/
tool_dev_url: https://github.com/Ecogenomics/GTDBTk
doi: "10.1093/bioinformatics/btz848"
licence: ["GNU General Public v3 (GPL v3)"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false, assembler:'spades' ]
- bins:
type: file
description: The binned fasta files from the assembler
pattern: "*.{fasta,fa}"
- database:
type: file
description: The local copy of the taxonomic database used by GTDB-tk (unzipped copy)
pattern: "*"
- mash_db:
type: file
description: The local copy of the Mash sketch database used by GTDB-tk if `ani_screen` mode is used (optional)
pattern: "*.msh"
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"
- summary:
type: file
description: A TSV summary file for the classification
pattern: "*.{summary.tsv}"
- tree:
type: file
description: NJ or UPGMA tree in Newick format produced from a multiple sequence alignment
pattern: "*.{classify.tree.gz}"
- markers:
type: file
description: A TSV summary file lineage markers used for the classification.
pattern: "*.{markers_summary.tsv}"
- msa:
type: file
description: Multiple sequence alignments file.
pattern: "*.{msa.fasta.gz}"
- user_msa:
type: file
description: Multiple sequence alignments file for the user-provided files.
pattern: "*.{user_msa.fasta.gz}"
- filtered:
type: file
description: A list of genomes with an insufficient number of amino acids in MSA..
pattern: "*.{filtered.tsv}"
- log:
type: file
description: GTDB-tk log file
pattern: "*.{log}"
- warnings:
type: file
description: GTDB-tk warnings log file
pattern: "*.{warnings.log}"
- failed:
type: file
description: A TSV summary of the genomes which GTDB-tk failed to classify.
pattern: "*.{failed_genomes.tsv}"
authors:
- "@skrakau"
- "@abhi18av"
maintainers:
- "@skrakau"
- "@abhi18av"