name: lofreq_call description: Lofreq subcommand to call low frequency variants from alignments keywords: - variant calling - low frequency variant calling - lofreq - lofreq/call tools: - lofreq: description: A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ 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 input file pattern: "*.{bam}" - fasta: type: file description: The reference fasta file output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - vcf: type: file description: VCF output file pattern: "*.{vcf}" authors: - "@bjohnnyd"