CI
f683dfcf8e
Build pipeline: viash-hub.htrnaseq.main-666pl
Source commit: 92755e84e7
Source message: Runner: output state and rework publishing (#68)
* add eset output param
* add outputs to publishing and runner
* update publishing
* Update publishing
* Remove debug statements
* Undo change to integration test script
* Add asserts
* Fix asserts and canonicalization of publish paths
* Move fData to folder
* Add CHANGELOG entry [ci skip]
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Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
22 lines
2.1 KiB
YAML
22 lines
2.1 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: "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"
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license: MIT
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keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
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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-resources/htrnaseq/v2
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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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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
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version: main
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organization: vsh
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