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4ed5e4eff3
* add liftOver module * add liftover module tests * fix getProcessName * fix tests * fix out of date function * version numbers should be numeric * drop versions.yml from test.yml * Update modules/ucsc/liftover/main.nf Remove software name variable Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update tests/modules/ucsc/liftover/main.nf Use test chain file Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * add genome_chain_gz to test data config * update md5sum for new chain test data * Fix indentation in file declaration Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
45 lines
1.1 KiB
YAML
45 lines
1.1 KiB
YAML
name: ucsc_liftover
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description: convert between genome builds
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keywords:
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- liftOver
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tools:
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- ucsc:
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description: Move annotations from one assembly to another
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homepage: http://hgdownload.cse.ucsc.edu/admin/exe/
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documentation: None
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tool_dev_url: None
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doi: ""
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licence: ['varies; see http://genome.ucsc.edu/license']
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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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- bed:
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type: file
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description: Browser Extensible Data (BED) file
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pattern: "*.{bed}"
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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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- version:
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type: file
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description: File containing software version
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pattern: "versions.yml"
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- lifted:
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type: file
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description: BED file containing successfully lifted variants
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pattern: "*.{lifted.bed}"
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- unlifted:
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type: file
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description: BED file containing variants that couldn't be lifted
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pattern: "*.{unlifted.bed}"
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authors:
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- "@nebfield"
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