mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 22:09:55 +00:00
75 lines
2.1 KiB
YAML
Generated
75 lines
2.1 KiB
YAML
Generated
name: kraken2_kraken2
|
|
description: Classifies metagenomic sequence data
|
|
keywords:
|
|
- classify
|
|
- metagenomics
|
|
- fastq
|
|
- db
|
|
tools:
|
|
- kraken2:
|
|
description: |
|
|
Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads
|
|
homepage: https://ccb.jhu.edu/software/kraken2/
|
|
documentation: https://github.com/DerrickWood/kraken2/wiki/Manual
|
|
doi: 10.1186/s13059-019-1891-0
|
|
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 FastQ files of size 1 and 2 for single-end and paired-end data,
|
|
respectively.
|
|
- db:
|
|
type: directory
|
|
description: Kraken2 database
|
|
- save_output_fastqs:
|
|
type: boolean
|
|
description: |
|
|
If true, optional commands are added to save classified and unclassified reads
|
|
as fastq files
|
|
- save_reads_assignment:
|
|
type: boolean
|
|
description: |
|
|
If true, an optional command is added to save a file reporting the taxonomic
|
|
classification of each input read
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- classified_reads_fastq:
|
|
type: file
|
|
description: |
|
|
Reads classified as belonging to any of the taxa
|
|
on the Kraken2 database.
|
|
pattern: "*{fastq.gz}"
|
|
- unclassified_reads_fastq:
|
|
type: file
|
|
description: |
|
|
Reads not classified to any of the taxa
|
|
on the Kraken2 database.
|
|
pattern: "*{fastq.gz}"
|
|
- classified_reads_assignment:
|
|
type: file
|
|
description: |
|
|
Kraken2 output file indicating the taxonomic assignment of
|
|
each input read
|
|
- report:
|
|
type: file
|
|
description: |
|
|
Kraken2 report containing stats about classified
|
|
and not classifed reads.
|
|
pattern: "*.{report.txt}"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@joseespinosa"
|
|
- "@drpatelh"
|