name: bamaligncleaner description: removes unused references from header of sorted BAM/CRAM files. keywords: - bam tools: - bamaligncleaner: description: Removes unaligned references in aligned BAM alignment file homepage: https://github.com/maxibor/bamAlignCleaner documentation: https://github.com/maxibor/bamAlignCleaner tool_dev_url: https://github.com/maxibor/bamAlignCleaner licence: ["GPL v3"] 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: Sorted BAM/CRAM file pattern: "*.{bam,cram}" authors: - "@jfy133"