name: pairtools_parse description: Find ligation junctions in .sam, make .pairs keywords: - parse tools: - pairtools: description: CLI tools to process mapped Hi-C data homepage: http://pairtools.readthedocs.io/ documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools doi: "" licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" - chromsizes: type: file description: chromosome size file 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" - pairsam: type: file description: parsed pair file pattern: "*.{pairsam.gz}" - stat: type: file description: stats of the pairs pattern: "*.{pairsam.stat}" authors: - "@jianhong"