name: kallistobustools_count
description: quantifies scRNA-seq data from fastq files using kb-python.
keywords:
  - scRNA-seq
  - count
  - single-cell
  - kallisto
  - bustools
tools:
  - kb:
      description: kallisto and bustools are wrapped in an easy-to-use program called kb
      homepage: https://www.kallistobus.tools/
      documentation: https://kb-python.readthedocs.io/en/latest/index.html
      tool_dev_url: https://github.com/pachterlab/kb_python
      licence: MIT License

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
        respectively.
  - index:
      type: file
      description: kb-ref index file (.idx)
      pattern: "*.{idx}"
  - t2g:
      type: file
      description: t2g file from kallisto
      pattern: "*t2g.txt"
  - t1c:
      type: file
      description: kb ref's c1 spliced_t2c file
      pattern: "*.{cdna_t2c.txt}"
  - t2c:
      type: file
      description: kb ref's c2 unspliced_t2c file
      pattern: "*.{introns_t2c.txt}"
  - workflow_mode:
      type: string
      description: String value defining workflow to use, can be one of "standard", "lamanno", "nucleus"
      pattern: "{standard,lamanno,nucleus,kite}"
  - technology:
      type: string
      description: String value defining the sequencing technology used.
      pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test']
  - count:
      type: file
      description: kb count output folder
      pattern: "*.{count}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@flowuenne"
