# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "trust4"
description: Run TRUST4 on RNA-seq data
keywords:
  - sort
  - example
  - genomics
tools:
  - "trust4":
      description: "TCR and BCR assembly from bulk or single-cell RNA-seq data"
      homepage: "https://github.com/liulab-dfci/TRUST4"
      documentation: "https://github.com/liulab-dfci/TRUST4"
      tool_dev_url: "https://github.com/liulab-dfci/TRUST4"
      licence: ["GPL v3"]
      identifier: biotools:trust4

input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - bam:
        type: file
        description: BAM file from bulk or single-cell RNA-seq data
        pattern: "*.bam"
    - reads:
        type: file
        description: List of input FastQ files of size 1 and 2 for single-end and paired-end
          data, respectively
  - - meta2:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - fasta:
        type: file
        description: Path to the fasta file coordinate and sequence of V/D/J/C genes
  - - meta3:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - vdj_reference:
        type: file
        description: reference file of V/D/J genes
  - - meta4:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - barcode_read:
        type: file
        description: barcode read file
  - - meta5:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - umi_read:
        type: file
        description: umi read file
output:
  - tsv:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "*.tsv":
          type: file
          description: tsv files created by TRUST4
          pattern: "*.tsv"
  - airr_files:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "*_airr.tsv":
          type: file
          description: TRUST4 results in AIRR format
          pattern: "*_airr.tsv"
  - airr_tsv:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - ${meta.id}_airr.tsv:
          type: file
          description: TRUST4 results in AIRR format
          pattern: "*_airr.tsv"
  - report_tsv:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "*_report.tsv":
          type: file
          description: TRUST4 report in tsv format
          pattern: "*_report.tsv"
  - fasta:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "*.fa":
          type: file
          description: Fasta files created by TRUST4
          pattern: "*.fa"
  - out:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "*.out":
          type: file
          description: Further report files
          pattern: "*.out"
  - fq:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "*.fq":
          type: file
          description: Fastq files created by TRUST4
          pattern: "*.fq"
  - outs:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "**":
          type: file
          description: outputt files
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@mapo9, @Joaodemeirelles"
maintainers:
  - "@mapo9"
