---
name: nacho_normalize
description: |
  NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data.
  NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes.
  Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target.
  As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.
keywords:
  - nacho
  - nanostring
  - mRNA
  - miRNA
  - qc
tools:
  - NACHO:
      description: |
        R package that uses two main functions to summarize and visualize NanoString RCC files,
        namely: `load_rcc()` and `visualise()`. It also includes a function `normalise()`, which (re)calculates
        sample specific size factors and normalises the data.
        For more information `vignette("NACHO")` and `vignette("NACHO-analysis")`
      homepage: https://github.com/mcanouil/NACHO
      documentation: https://cran.r-project.org/web/packages/NACHO/vignettes/NACHO.html
      doi: "10.1093/bioinformatics/btz647"
      licence: ["GPL-3.0"]
      identifier: ""
      args_id: "$args"

input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test' ]
    - rcc_files:
        type: file
        description: |
          List of RCC files for all samples, which are direct outputs from NanoString runs
        pattern: "*.RCC"
  - - meta2:
        type: map
        description: |
          Groovy Map containing file information
          e.g. [ id:'test_samplesheet' ]
    - sample_sheet:
        type: "file"
        pattern: "*.csv"
        description: |
          Comma-separated file with 3 columns: RCC_FILE, RCC_FILE_NAME, and SAMPLE_ID

output:
  - normalized_counts:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "normalized_counts.tsv":
          type: file
          description: |
            Tab-separated file with gene normalized counts for the samples
          pattern: "normalized_counts.tsv"

  - normalized_counts_wo_HK:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "normalized_counts_wo_HKnorm.tsv":
          type: file
          description: |
            Tab-separated file with gene normalized counts for the samples, without housekeeping genes.
          pattern: "normalized_counts_wo_HKnorm.tsv"
  - versions:
      - "versions.yml":
          type: file
          description: |
            File containing software versions
          pattern: "versions.yml"

authors:
  - "@alanmmobbs93"
maintainers:
  - "@alanmmobbs93"
