The merge module merges structural variants within one or more vcf files.
Input
name:type
description
pattern
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
vcfs:list
One or more VCF files. The order and number of files should correspond to
the order and number of tags in the priority input channel.
*.{vcf,vcf.gz}
input_priority:list
Prioritize the input VCF files according to this list,
e.g [‘tiddit’,‘cnvnator’]. The order and number of tags should correspond to
the order and number of VCFs in the vcfs input channel.
sort_inputs:boolean
Should the input files be sorted by name. The priority tag will be sorted
together with it’s corresponding VCF file.
Output
name:type
description
pattern
vcf
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.{vcf,vcf.gz,bcf,bcf.gz}:file
VCF output file
*.{vcf,vcf.gz,bcf,bcf.gz}
tbi
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.tbi:file
Alternative VCF file index
*.tbi
csi
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
