name: isoseq3_refine description: Generate transcripts by clustering HiFi reads keywords: - isoseq3 - isoseq3/refine tools: - isoseq3: description: IsoSeq3 - Scalable De Novo Isoform Discovery homepage: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md doi: "" licence: ['BSD-3-Clause-Clear'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test ] - bam: type: file description: BAM file, cleaned ccs generated by lima pattern: "*.bam" - primers: type: file description: fasta file of primers pattern: "*.fasta" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test' ] - bam: type: file description: Set of complete reads (with polyA tail), where the polyA has been trimmed pattern: "*.bam" - pbi: type: file description: Pacbio index file from polyA trimmed reads pattern: "*.pbi" - consensusreadset: type: file description: Metadata about read library pattern: "*.xml" - summary: type: file description: json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads pattern: "*.json" - report: type: file description: Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name) pattern: "*.csv" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@sguizard"