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* Add kraken2 run module * Add kraken2 run module * Add coronavirus kraken2 db * Adding kraken2 run tests * Update software/kraken2/run/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Fixing files commited by mistake * Remove params for meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
59 lines
1.7 KiB
YAML
59 lines
1.7 KiB
YAML
name: kraken2_run
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description: Classifies metagenomic sequence data
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keywords:
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- classify
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- metagenomics
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- fastq
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- db
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tools:
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- kraken2:
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description: |
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Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads
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homepage: https://ccb.jhu.edu/software/kraken2/
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documentation: https://github.com/DerrickWood/kraken2/wiki/Manual
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doi: 10.1186/s13059-019-1891-0
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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 ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- db:
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type: directory
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description: Kraken2 database
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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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- classified:
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type: file
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description: |
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Reads classified to belong to any of the taxa
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on the Kraken2 database.
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pattern: "*{fastq.gz}"
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- unclassified:
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type: file
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description: |
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Reads not classified to belong to any of the taxa
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on the Kraken2 database.
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pattern: "*{fastq.gz}"
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- txt:
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type: file
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description: |
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Kraken2 report containing stats about classified
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and not classifed reads.
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pattern: "*.{report.txt}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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