name: ivar_trim description: Trim primer sequences rom a BAM file with iVar keywords: - amplicon sequencing - trimming - fasta tools: - ivar: description: | iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: Co-ordinate sorted BAM file pattern: "*.bam" - bai: type: file description: Index file for co-ordinate sorted BAM file pattern: "*.bai" - bed: type: file description: BED file with primer labels and positions pattern: "*.bed" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: iVar generated trimmed bam file (unsorted) pattern: "*.bam" - log: type: file description: Log file generated by iVar for use with MultiQC pattern: "*.log" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@andersgs" - "@drpatelh"