name: bcftools_stats description: Generates stats from VCF files keywords: - variant calling - stats - VCF tools: - stats: description: | Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using plot-vcfstats. homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 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 ] - vcf: type: file description: VCF input file pattern: "*.{vcf}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - stats: type: file description: Text output file containing stats pattern: "*.{txt}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@joseespinosa" - "@drpatelh"