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3868c3ab4b
* initial commit [ci skip] * reuse the modules code from nf-core/mag [ci skip] * add contextual information for the module [ci skip] * add stubs to avoid downloading db [ci skip] * trigger test * iterate on tests [ci skip] * itereate tests [ci skip] * add bins [ci skip] * fix stubs [ci skip] * interation on tests with stubs [ci skip] * use the existing pattern and fasta for input * accomodate the new version file format * use variable for the stub [ci skip] * update the versions file in meta.yml * Accomodate code review regarding publishDir function [ci skip] Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * remove extra newline * use bioconda channel * update the description for filtered file * Apply suggestions from code review * Update main.nf * Update main.nf * Update modules/gtdbtk/classifywf/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
78 lines
2.6 KiB
YAML
78 lines
2.6 KiB
YAML
name: gtdbtk_classifywf
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description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.
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keywords:
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- GTDB taxonomy
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- taxonomic classification
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tools:
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- gtdbtk:
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description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.
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homepage: https://ecogenomics.github.io/GTDBTk/
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documentation: https://ecogenomics.github.io/GTDBTk/
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tool_dev_url: https://github.com/Ecogenomics/GTDBTk
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doi: "10.1093/bioinformatics/btz848"
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licence: ['GNU General Public v3 (GPL v3)']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false, assembler:'spades' ]
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- bins:
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type: The binned fasta files from the assembler
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description: Fasta files
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pattern: "*.{fasta,fa}"
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- database:
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type: The local copy of the taxonomic database used by GTDB-tk
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description: The unzipped copy of the database
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pattern: "*"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- summary:
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type: file
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description: A TSV summary file for the classification
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pattern: "*.{summary.tsv}"
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- tree:
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type: file
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description: NJ or UPGMA tree in Newick format produced from a multiple sequence alignment
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pattern: "*.{classify.tree.gz}"
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- markers:
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type: file
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description: A TSV summary file lineage markers used for the classification.
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pattern: "*.{markers_summary.tsv}"
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- msa:
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type: file
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description: Multiple sequence alignments file.
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pattern: "*.{msa.fasta.gz}"
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- user_msa:
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type: file
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description: Multiple sequence alignments file for the user-provided files.
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pattern: "*.{user_msa.fasta.gz}"
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- filtered:
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type: file
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description: A list of genomes with an insufficient number of amino acids in MSA..
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pattern: "*.{filtered.tsv}"
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- log:
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type: file
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description: GTDB-tk log file
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pattern: "*.{log}"
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- warnings:
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type: file
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description: GTDB-tk warnings log file
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pattern: "*.{warnings.log}"
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- failed:
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type: file
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description: A TSV summary of the genomes which GTDB-tk failed to classify.
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pattern: "*.{failed_genomes.tsv}"
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authors:
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- "@skrakau"
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- "@abhi18av"
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