name: lofreq_callparallel description: It predicts variants using multiple processors keywords: - call - variants tools: - lofreq: description: Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's call-parallel programme predicts variants using multiple processors homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/ doi: "10.1093/nar/gks918" licence: ['MIT'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test' ] - bam: type: file description: Sorted BAM file pattern: "*.{bam}" - bai: type: file description: BAM index file pattern: "*.{bai}" - fasta: type: file description: Reference genome FASTA file pattern: "*.{fasta}" - fai: type: file description: Reference genome FASTA index file pattern: "*.{fai}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - version: type: file description: File containing software version pattern: "*.{version.txt}" - vcf: type: file description: Predicted variants file pattern: "*.{vcf}" authors: - "@kaurravneet4123" - "@bjohnnyd"