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:false ]
*.{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:false ]
*.tbi
:file
Alternative VCF file index
*.tbi
csi
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.csi
:file
Default VCF file index
*.csi
versions_svdb
${task.process}
:string
The name of the process
svdb
:string
The name of the tool
svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\1/p'
:eval
The expression to obtain the version of the tool
versions_bcftools
${task.process}
:string
The name of the process
bcftools
:string
The tool name
bcftools --version | sed '1!d; s/^.*bcftools //'
:eval
The command used to generate the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
svdb
:string
The name of the tool
svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\1/p'
:eval
The expression to obtain the version of the tool
${task.process}
:string
The name of the process
bcftools
:string
The tool name
bcftools --version | sed '1!d; s/^.*bcftools //'
:eval
The command used to generate the version of the tool
