name: isoseq3_cluster description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences keywords: - cluster tools: - isoseq3: description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences 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 generated by isoseq3 refine pattern: "*.bam" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - version: type: file description: File containing software version pattern: "versions.yml" - bam: type: file description: BAM file of clustered consensus pattern: "*.transcripts.bam" - pbi: type: file description: Pacbio Index of consensus reads generated by clustering pattern: "*.transcripts.bam.pbi" - cluster: type: file description: A two columns (from, to) file describing original read name to new read name pattern: "*.transcripts.cluster" - cluster_report: type: file description: A table files clusters (transcripts) members (read) pattern: "*.transcripts.cluster_report.csv" - transcriptset: type: file description: A metadata xml file which contains full paths to data files pattern: "*.transcripts.transcriptset.xml" - hq_bam: type: file description: High quality reads (when --use-qvs is set) pattern: "*.transcripts.hq.bam" - hq_pbi: type: file description: Pacbio index of high quality reads (when --use-qvs is set) pattern: "*.transcripts.hq.bam.pbi" - lq_bam: type: file description: Low quality reads (when --use-qvs is set) pattern: "*.transcripts.lq.bam" - lq_pbi: type: file description: Pacbio index of low quality reads (when --use-qvs is set) pattern: "*.transcripts.lq.bam.pbi" - singletons_bam: type: file description: Unclustered reads (when --singletons is set) pattern: "*.transcripts.singletons.bam" - singletons_pbi: type: file description: Pacbio index of unclustered reads (when --singletons is set) pattern: "*.transcripts.singletons.bam.pbi" authors: - "@sguizard"