name: ivar_variants description: Call variants from a BAM file using iVar keywords: - amplicon sequencing - variants - 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 licence: ['GPL-3.0-or-later'] 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" - gff: type: file description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done. patter: "*.gff" - save_mpileup: type: boolean description: Save mpileup file generated by ivar variants output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - tsv: type: file description: iVar generated TSV file with the variants pattern: "*.tsv" - 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"