name: leehom description: Bayesian reconstruction of ancient DNA fragments keywords: - ancient DNA - adapter removal - clipping - trimming - merging - collapsing - preprocessing - bayesian tools: - leehom: description: Bayesian reconstruction of ancient DNA fragments homepage: "https://grenaud.github.io/leeHom/" documentation: "https://github.com/grenaud/leeHom" tool_dev_url: "https://github.com/grenaud/leeHom" doi: "10.1093/nar/gku699" licence: ['GPL v3'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: Unaligned BAM or one or two gzipped FASTQ file(s) pattern: "*.{bam,fq.gz,fastq.gz}" 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" - bam: type: file description: BAM file pattern: "*.bam" - fq_pass: type: file description: Trimmed and merged FASTQ pattern: "*.fq.gz" - fq_fail: type: file description: Failed trimmed and merged FASTQs pattern: "*.fail.fq.gz" - unmerged_r1_fq_pass: type: file description: Passed unmerged R1 FASTQs pattern: "*.r1.fq.gz" - unmerged_r1_fq_fail: type: file description: Failed unmerged R1 FASTQs pattern: "*.r1.fail.fq.gz" - unmerged_r2_fq_pass: type: file description: Passed unmerged R1 FASTQs pattern: "*.r2.fq.gz" - unmerged_r2_fq_pass: type: file description: Failed unmerged R1 FASTQs pattern: "*.r2.fail.fq.gz" - log: type: file description: Log file of command pattern: "*.log" authors: - "@jfy133"