mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-25 07:29:56 +00:00
78 lines
2.3 KiB
YAML
Generated
78 lines
2.3 KiB
YAML
Generated
name: "krakenuniq_preloadedkrakenuniq"
|
|
description: Classifies metagenomic sequence data using unique k-mer counts
|
|
keywords:
|
|
- classify
|
|
- metagenomics
|
|
- kmers
|
|
- fastq
|
|
- db
|
|
tools:
|
|
- "krakenuniq":
|
|
description: "Metagenomics classifier with unique k-mer counting for more specific results"
|
|
homepage: https://github.com/fbreitwieser/krakenuniq
|
|
documentation: https://github.com/fbreitwieser/krakenuniq
|
|
doi: 10.1186/s13059-018-1568-0
|
|
licence: ["MIT"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- fastqs:
|
|
type: file
|
|
description: List of input FastQ files
|
|
- db:
|
|
type: directory
|
|
description: KrakenUniq database
|
|
- ram_chunk_size:
|
|
type: val
|
|
description: Amount of maximum amount of RAM each chunk of database that should be loaded at any one time
|
|
pattern: "*GB"
|
|
- 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 KrakenUniq database.
|
|
pattern: "*.fastq.gz"
|
|
- unclassified_reads_fastq:
|
|
type: file
|
|
description: |
|
|
Reads not classified to any of the taxa
|
|
on the KrakenUniq database.
|
|
pattern: "*.fastq.gz"
|
|
- classified_assignment:
|
|
type: file
|
|
description: |
|
|
KrakenUniq output file indicating the taxonomic assignment of
|
|
each input read ## DOUBLE CHECK!!
|
|
- report:
|
|
type: file
|
|
description: |
|
|
KrakenUniq report containing stats about classified
|
|
and not classifed reads.
|
|
pattern: "*.report.txt"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@mjamy"
|
|
- "@Midnighter"
|