2022-04-02 15:02:05 +00:00
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name: bbmap_bbduk
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description: Adapter and quality trimming of sequencing reads
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keywords:
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- trimming
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- adapter trimming
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- quality trimming
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2022-09-08 06:08:36 +00:00
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- fastq
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2022-04-02 15:02:05 +00:00
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tools:
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- bbmap:
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description: BBMap is a short read aligner, as well as various other bioinformatic tools.
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homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
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documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
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tool_dev_url: None
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doi: ""
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licence: ["UC-LBL license (see package)"]
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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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- contaminants:
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type: file
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description: |
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Reference files containing adapter and/or contaminant sequences for sequence kmer matching
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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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- reads:
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type: file
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description: The trimmed/modified fastq reads
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pattern: "*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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- log:
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type: file
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description: Bbduk log file
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pattern: "*bbduk.log"
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authors:
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- "@MGordon09"
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