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40 lines
1.2 KiB
YAML
40 lines
1.2 KiB
YAML
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name: khmer_normalizebymedian
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description: Module that calls normalize-by-median.py from khmer. The module can take a mix of paired end (interleaved) and single end reads. If both types are provided, only a single file with single ends is possible.
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keywords:
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- digital normalization
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- khmer
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tools:
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- khmer:
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description: khmer k-mer counting library
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homepage: https://github.com/dib-lab/khmer
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documentation: https://khmer.readthedocs.io/en/latest/
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tool_dev_url: https://github.com/dib-lab/khmer
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doi: "https://doi.org/10.12688/f1000research.6924.1"
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licence: ['BSD License']
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input:
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- pe_reads:
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type: files
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description: Paired-end interleaved fastq files
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pattern: "*.{fq,fastq}.gz"
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- se_reads:
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type: files
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description: Single-end fastq files
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pattern: "*.{fq,fastq}.gz"
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- name:
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type: string
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description: filename for output file(s); ".fastq.gz" will be appended
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output:
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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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- reads:
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type: file
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description: Interleaved fastq files
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pattern: "*.{fq,fastq}.gz"
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authors:
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- "@erikrikarddaniel"
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