name: freebayes description: A haplotype-based variant detector keywords: - variant caller - SNP - genotyping - somatic variant calling - germline variant calling - bacterial variant calling - bayesian tools: - freebayes: description: Bayesian haplotype-based polymorphism discovery and genotyping homepage: https://github.com/freebayes/freebayes documentation: https://github.com/freebayes/freebayes tool_dev_url: https://github.com/freebayes/freebayes doi: "arXiv:1207.3907" licence: ['MIT'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - input: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" - input_index: type: file description: BAM/CRAM/SAM index file pattern: "*.bam.bai" - fasta: type: file description: reference fasta file pattern: ".{fa,fa.gz,fasta,fasta.gz}" - fasta_fai: type: file description: reference fasta file index pattern: "*.{fa,fasta}.fai" - targets: type: file description: Optional - Limit analysis to targets listed in this BED-format FILE. pattern: "*.bed" - samples: type: file description: Optional - Limit analysis to samples listed (one per line) in the FILE. pattern: "*.txt" - populations: type: file description: Optional - Each line of FILE should list a sample and a population which it is part of. pattern: "*.txt" - cnv: type: file description: | A copy number map BED file, which has either a sample-level ploidy: sample_name copy_number or a region-specific format: seq_name start end sample_name copy_number pattern: "*.bed" 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: Compressed VCF file pattern: "*.vcf.gz" authors: - "@maxibor" - "@FriederikeHanssen" - "@maxulysse"