name: ivar_consensus description: Generate a consensus sequence from a BAM file using iVar keywords: - amplicon sequencing - consensus - 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: A sorted (with samtools sort) and trimmed (with iVar trim) bam file pattern: "*.bam" - fasta: type: file description: The reference sequence used for mapping and generating the BAM file pattern: "*.fa" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fasta: type: file description: iVar generated consensus sequence pattern: "*.fa" - qual: type: file description: iVar generated quality file pattern: "*.qual.txt" - mpileup: type: file description: mpileup output from samtools mpileup [OPTIONAL] pattern: "*.mpileup" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@andersgs" - "@drpatelh"