HiFi-based caller for highly homologous genes
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:true ]
[ id:'sample1', single_end:true ]
bam{:bash}
:file
Sorted BAM file
*.bam
bai{:bash}
Index of BAM file
*.bai
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta{:bash}
The reference fasta file
*.fasta
meta3{:bash}
Groovy Map containing config information e.g. [ id:‘config’ ]
config{:bash}
Config file
*.yaml
json{:bash}
*.paraphase.json{:bash}
Summary of haplotype and variant calls
*.paraphase.json
*.paraphase.bam{:bash}
(re)aligned BAM file
*.paraphase.bam
*.paraphase.bam.bai{:bash}
Index of (re)aligned BAM file
*.paraphase.bam.bai
vcf{:bash}
${prefix}_paraphase_vcfs/*.vcf.gz{:bash}
compressed VCF file(s) per gene
*.vcf.gz
vcf_index{:bash}
${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}{:bash}
compressed VCF file index
*.vcf.gz.{tbi,csi}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
