HiFi-based caller for highly homologous genes
meta
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:true ]
[ id:'sample1', single_end:true ]
bam
:file
Sorted BAM file
*.bam
bai
Index of BAM file
*.bai
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta
The reference fasta file
*.fasta
meta3
Groovy Map containing config information e.g. [ id:‘config’ ]
config
Config file
*.yaml
json
*.paraphase.json
Summary of haplotype and variant calls
*.paraphase.bam
(re)aligned BAM file
*.paraphase.bam.bai
Index of (re)aligned BAM file
vcf
${prefix}_paraphase_vcfs/*.vcf.gz
compressed VCF file(s) per gene
*.vcf.gz
vcf_index
${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}
compressed VCF file index
*.vcf.gz.{tbi,csi}
versions_minimap2
${task.process}
:string
The name of the process
minimap2
The name of the tool
minimap2 --version
:eval
The expression to obtain the version of the tool
versions_paraphase
paraphase
paraphase --version
versions_samtools
samtools
samtools version | sed '1!d;s/.* //'
versions
