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53 lines
1.5 KiB
YAML
53 lines
1.5 KiB
YAML
name: bbmap_align
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description: Align short or PacBio reads to a reference genome using BBMap
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keywords:
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- align
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- map
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- fasta
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- fastq
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- genome
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- reference
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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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- fastq:
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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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- ref:
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type: file
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description: |
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Either "ref" a directory containing an index, the name of another directory
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with a "ref" subdirectory containing an index or the name of a fasta formatted
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nucleotide file containg the reference to map to.
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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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- 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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- bam:
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type: file
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description: BAM file
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pattern: "*.{bam}"
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authors:
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- "@erikrikarddaniel"
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