name: lofreq_indelqual description: Inserts indel qualities in a BAM file keywords: - bam - indel - qualities tools: - lofreq: description: Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file homepage: 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', single_end:false ] - bam: type: file description: BAM file pattern: "*.{bam}" - fasta: type: file description: Reference genome FASTA file pattern: "*.{fasta}" 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: "versions.yml" - bam: type: file description: BAM file with indel qualities inserted into it pattern: "*.{bam}" authors: - "@kaurravneet4123"