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75 lines
2 KiB
YAML
75 lines
2 KiB
YAML
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name: spades
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description: Assembles a small genome (bacterial, fungal, viral)
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keywords:
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- genome
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- assembly
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- genome assembler
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- small genome
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- de novo assembler
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tools:
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- spades:
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description: SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
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homepage: http://cab.spbu.ru/files/release3.15.0/manual.html
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documentation: http://cab.spbu.ru/files/release3.15.0/manual.html
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tool_dev_url: https://github.com/ablab/spades
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doi: 10.1089/cmb.2012.0021
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licence: ['GPL v2']
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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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- hmm:
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type: file
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description:
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File or directory with amino acid HMMs for Spades HMM-guided mode.
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- coronaspades:
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type: boolean
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description: |
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Run coronaspades instead of default spades mode. coronaSPAdes is a special
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mode of rnaviralSPAdes specifically aimed for SARS-CoV-2 de novo assembly.
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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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- scaffolds:
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type: file
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description: |
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Fasta file containing scaffolds
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- contigs:
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type: file
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description: |
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Fasta file containing contigs
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- transcripts:
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type: file
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description: |
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Fasta file containing transcripts
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- gene_clusters:
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type: file
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description: |
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Fasta file containing gene_clusters
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- gfa:
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type: file
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description: |
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gfa file containing assembly
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- log:
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type: file
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description: |
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Spades log file
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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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