name: htrnaseq
summary: |
  A workflow for high-throughput RNA-seq data analyses.
description: |
  This workflow is designed to process high-throughput RNA-seq data, where every
  well of a microarray plate is a sample. A fasta file provided as input
  defines the mapping between sample barcodes and wells.

  The workflow is built in a modular fashion, where most of the base functionality
  is provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)
  supplemented by custom base components and workflow components in this package.

  The full workflow is split in two major subworkflows that can be run independently:

  * **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.
  * **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.

  Each of those can be started individually, or the full workflow can be run in two ways:

  1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) 
  containing the main functionality.
  2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a
  number of choices (input/output structure and location) have been made.

  Input for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running
  [demultiplex](https://www.viash-hub.com/packages/demultiplex) first.

license: MIT
keywords:
  [
    bioinformatics,
    sequencing,
    high-throughput,
    RNAseq,
    mapping,
    counting,
    pipeline,
    workflow,
  ]
links:
  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
  repository: https://github.com/viash-hub/htrnaseq

viash_version: 0.9.4

info:
  test_resources:
    - path: gs://viash-hub-resources/htrnaseq/v1
      dest: resources_test

config_mods: |
  .requirements.commands := ['ps']
  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}