diff --git a/software/ivar/variants/meta.yml b/software/ivar/variants/meta.yml new file mode 100644 index 00000000..2b815ec1 --- /dev/null +++ b/software/ivar/variants/meta.yml @@ -0,0 +1,68 @@ +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 +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. +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 ] + - variants: + type: file + description: iVar generated TSV file with the variants + pattern: "*.tsv" + - mpileup: + type: file + description: mpileup output from samtools mpileup [OPTIONAL] + pattern: "*.mpileup" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@andersgs" + - "@drpatelh"