nf-core_modules/modules/delly/call/meta.yml
nvnieuwk 5a30294eec
Update for the delly/call module (#2008)
* 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>
2022-09-05 12:09:55 +02:00

66 lines
1.7 KiB
YAML

name: delly_call
description: Call structural variants
keywords:
- genome
- structural
- variants
- bcf
tools:
- delly:
description: Structural variant discovery by integrated paired-end and split-read analysis
homepage: https://github.com/dellytools/delly
documentation: https://github.com/dellytools/delly/blob/master/README.md
tool_dev_url: None
doi: "DOI:10.1093/bioinformatics/bts378"
licence: ["BSD-3-Clause"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked
pattern: "*.{bam,cram}"
- bai:
type: file
description: Index of the BAM/CRAM file
pattern: "*.{bai,crai}"
- exclude_bed:
type: file
description: An optional bed file containing regions to exclude from the called VCF
pattern: "*.bed"
- fasta:
type: file
description: The reference fasta file
pattern: "*.{fasta,fa}"
- fai:
type: file
description: Index of reference fasta file to identify split-reads
pattern: "*.fai"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bcf:
type: file
description: Called variants in BCF format
pattern: "*.{bcf}"
- csi:
type: file
description: A generated csi index that matches the bcf output
pattern: "*.{bcf.csi}"
authors:
- "@projectoriented"
- "@nvnieuwk"