CI
69b6860b63
Build pipeline: viash-hub.htrnaseq.main-6pfd6
Source commit: 28e59b1fb7
Source message: Update readme (#54)
55 lines
2.0 KiB
YAML
55 lines
2.0 KiB
YAML
name: htrnaseq
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summary: |
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A workflow for high-throughput RNA-seq data analyses.
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description: |
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This workflow is designed to process high-throughput RNA-seq data, where every
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well of a microarray plate is a sample. A fasta file provided as input
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defines the mapping between sample barcodes and wells.
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The workflow is built in a modular fashion, where most of the base functionality
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is provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)
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supplemented by custom base components and workflow components in this package.
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The full workflow is split in two major subworkflows that can be run independently:
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* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.
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* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.
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Each of those can be started individually, or the full workflow can be run in two ways:
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1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq)
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containing the main functionality.
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2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a
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number of choices (input/output structure and location) have been made.
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Input for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running
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[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.
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license: MIT
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keywords:
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[
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bioinformatics,
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sequencing,
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high-throughput,
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RNAseq,
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mapping,
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counting,
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pipeline,
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workflow,
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]
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links:
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issue_tracker: https://github.com/viash-hub/htrnaseq/issues
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repository: https://github.com/viash-hub/htrnaseq
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viash_version: 0.9.4
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info:
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test_resources:
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- path: gs://viash-hub-test-data/htrnaseq/v1/
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dest: resources_test
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config_mods: |
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.requirements.commands := ['ps']
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.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
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.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
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