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"