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3f4eccbf0f
* testing works but need to fix paths and add exclude list * edited meta file and removed TODOs * left over TODOs * test passed, final push * resolving initial comments * Update software/delly/call/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
55 lines
1.4 KiB
YAML
55 lines
1.4 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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- bam:
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type: file
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description: BAM file from alignment must be sorted, indexed, and duplicate marked
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pattern: "*.{bam}"
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- fasta:
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type: file
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description: The reference fasta file
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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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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: "*.{version.txt}"
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- bcf:
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type: file
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description: 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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