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52 lines
1.3 KiB
YAML
52 lines
1.3 KiB
YAML
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name: "scramble_clusteridentifier"
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description: The cluster_identifier tool of Scramble identifies soft clipped clusters
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keywords:
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- bam
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- cram
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- soft-clipped clusters
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tools:
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- "scramble":
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description: "Soft Clipped Read Alignment Mapper"
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homepage: "https://github.com/GeneDx/scramble"
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documentation: "https://github.com/GeneDx/scramble"
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tool_dev_url: "https://github.com/GeneDx/scramble"
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doi: ""
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licence: "['CC']"
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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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- input:
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type: file
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description: BAM/CRAM file
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pattern: "*.{bam,cram}"
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- input_index:
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type: file
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description: Index of the BAM/CRAM file
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pattern: "*.{bai,crai}"
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- fasta:
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type: file
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description: The reference FASTA file (mandatory when using CRAM files)
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pattern: "*.{fasta,fa}"
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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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- clusters:
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type: file
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description: Tab-delimited file containing the soft-clipped clusters
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pattern: "*.clusters.txt"
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authors:
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- "@nvnieuwk"
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