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Build branch htrnaseq/main with version main to htrnaseq on branch main (92755e8)

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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]

---------

Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
This commit is contained in:
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2025-09-02 08:17:05 +00:00
parent b51996294b
commit f683dfcf8e
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_viash.yaml
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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.
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,
]
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")'
.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