modules/paragraph_multigrmpy

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

A VCF or JSON file containing called structural variants

The index for the VCF file

BAM or CRAM file(s) to genotype against. These should be specified inside the manifest

The index/indices for the BAM/CRAM file(s)

A tab separated file containing information on the BAM/CRAM files.
This information can be generated using paragraph/idxdepth.
More information can be found here: https://github.com/Illumina/paragraph#sample-manifest

Groovy Map containing sample information for the FASTA file
e.g. [ id:‘test’, single_end

The reference FASTA file used to generate the VCF and BAM/CRAM files

Groovy Map containing sample information for the FASTA index file
e.g. [ id:‘test’, single_end

The index of the reference FASTA file