name: variantbam description: Filtering, downsampling and profiling alignments in BAM/CRAM formats keywords: - filter - bam - subsample - downsample - downsample bam - subsample bam tools: - variantbam: description: Filtering and profiling of next-generational sequencing data using region-specific rules homepage: https://github.com/walaj/VariantBam documentation: https://github.com/walaj/VariantBam#table-of-contents tool_dev_url: https://github.com/walaj/VariantBam doi: 10.1093/bioinformatics/btw111 licence: ['Apache2'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - bam: type: file description: Filtered or downsampled BAM file pattern: "*.{bam}" authors: - "@bjohnnyd"