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* Add centrifuge module * Add centrifuge module * Add centrifuge module * Add centrifuge module
73 lines
1.9 KiB
YAML
73 lines
1.9 KiB
YAML
name: centrifuge
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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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- centrifuge:
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description: Centrifuge is a classifier for metagenomic sequences.
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homepage: https://ccb.jhu.edu/software/centrifuge/
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documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
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doi: 10.1101/gr.210641.116
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licence: ["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 ]
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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: Centrifuge database in .tar.gz format
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pattern: "*.tar.gz"
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- save_unaligned:
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type: value
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description: If true unmapped fastq files are saved
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- save_aligned:
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type: value
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description: If true mapped fastq files are saved
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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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- report:
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type: file
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description: |
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File containing a classification summary
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pattern: "*.{report.txt}"
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- results:
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type: file
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description: |
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File containing classification results
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pattern: "*.{results.txt}"
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- kreport:
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type: file
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description: |
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File containing kraken-style report from centrifuge
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out files.
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pattern: "*.{kreport.txt}"
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- fastq_unmapped:
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type: file
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description: Unmapped fastq files
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pattern: "*.unmapped.fastq.gz"
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- fastq_mapped:
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type: file
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description: Mapped fastq files
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pattern: "*.mapped.fastq.gz"
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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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authors:
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- "@sofstam"
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- "@jfy133"
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- "@sateeshperi"
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