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5a30294eec
* updated the delly/call module * Update modules/delly/call/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
66 lines
1.7 KiB
YAML
66 lines
1.7 KiB
YAML
name: delly_call
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description: Call structural variants
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keywords:
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- genome
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- structural
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- variants
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- bcf
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tools:
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- delly:
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description: Structural variant discovery by integrated paired-end and split-read analysis
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homepage: https://github.com/dellytools/delly
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documentation: https://github.com/dellytools/delly/blob/master/README.md
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tool_dev_url: None
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doi: "DOI:10.1093/bioinformatics/bts378"
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licence: ["BSD-3-Clause"]
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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 from alignment must be sorted, indexed, and duplicate marked
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pattern: "*.{bam,cram}"
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- bai:
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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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- exclude_bed:
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type: file
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description: An optional bed file containing regions to exclude from the called VCF
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pattern: "*.bed"
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.{fasta,fa}"
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- fai:
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type: file
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description: Index of reference fasta file to identify split-reads
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pattern: "*.fai"
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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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- bcf:
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type: file
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description: Called variants in BCF format
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pattern: "*.{bcf}"
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- csi:
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type: file
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description: A generated csi index that matches the bcf output
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pattern: "*.{bcf.csi}"
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authors:
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- "@projectoriented"
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- "@nvnieuwk"
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