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\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
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/v2
      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'}
  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
version: main
organization: vsh