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68 lines
1.9 KiB
YAML
68 lines
1.9 KiB
YAML
name: quast
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description: Quality Assessment Tool for Genome Assemblies
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keywords:
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- quast
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- assembly
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- quality
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tools:
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- quast:
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description: |
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QUAST calculates quality metrics for genome assemblies
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homepage: http://bioinf.spbau.ru/quast
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doi:
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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input:
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- consensus:
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type: file
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description: |
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Fasta file containing the assembly of interest
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- fasta:
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type: file
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description: |
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The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.
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- use_fasta:
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type: boolean
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description: Whether to use a fasta reference
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- gff:
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type: file
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description: The genome GFF file. Has to contain at least a non-empty string dummy value.
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- use_gff:
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type: boolean
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description: Whether to use the provided gff reference annotation file
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output:
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- quast:
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type: directory
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description: Directory containing complete quast report
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pattern: "{prefix}.lineage_report.csv"
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- report:
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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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- "@drpatelh"
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- "@kevinmenden"
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