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8ce6810787
* fix: remove left-over unnecessary code * Update DASTool * Fix tests * Fix test.ymls * Fix container build version * Make tests less strict to account for variability * Apply suggestions from code review Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Add missing description Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
103 lines
2.8 KiB
YAML
103 lines
2.8 KiB
YAML
name: dastool_dastool
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description: DAS Tool binning step.
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keywords:
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- binning
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- das tool
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- table
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- de novo
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- bins
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- contigs
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- assembly
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- das_tool
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tools:
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- dastool:
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description: |
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DAS Tool is an automated method that integrates the results
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of a flexible number of binning algorithms to calculate an optimized, non-redundant
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set of bins from a single assembly.
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homepage: https://github.com/cmks/DAS_Tool
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documentation: https://github.com/cmks/DAS_Tool
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tool_dev_url: https://github.com/cmks/DAS_Tool
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doi: "10.1038/s41564-018-0171-1"
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licence: ["BSD"]
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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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- contigs:
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type: file
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description: fasta file
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pattern: "*.{fa.gz,fas.gz,fasta.gz}"
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- bins:
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type: file
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description: "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin"
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pattern: "*.tsv"
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- proteins:
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type: file
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description: Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)
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pattern: "*.{fa.gz,fas.gz,fasta.gz}"
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- db_directory:
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type: file
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description: (optional) Directory of single copy gene 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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- version:
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type: file
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description: File containing software version
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pattern: "versions.yml"
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- log:
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type: file
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description: Log file of the run
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pattern: "*.log"
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- summary:
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type: file
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description: Summary of output bins including quality and completeness estimates
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pattern: "*summary.txt"
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- contig2bin:
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type: file
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description: Scaffolds to bin file of output bins
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pattern: "*.contig2bin.txt"
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- eval:
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type: file
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description: Quality and completeness estimates of input bin sets
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pattern: "*.eval"
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- bins:
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description: Final refined bins in fasta format
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pattern: "*.fa"
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- pdfs:
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type: file
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description: Plots showing the amount of high quality bins and score distribution of bins per method
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pattern: "*.pdf"
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- fasta_proteins:
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type: file
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description: Output from prodigal if not already supplied
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pattern: "*.proteins.faa"
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- fasta_archaea_scg:
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type: file
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description: Results of archaeal single-copy-gene prediction
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pattern: "*.archaea.scg"
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- fasta_bacteria_scg:
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type: file
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description: Results of bacterial single-copy-gene prediction
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pattern: "*.bacteria.scg"
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- b6:
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type: file
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description: Results in b6 format
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pattern: "*.b6"
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- seqlength:
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type: file
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description: Summary of contig lengths
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pattern: "*.seqlength"
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authors:
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- "@maxibor"
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- "@jfy133"
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