viash_version: 0.9.7
version: v4.1.0
source: src
target: target
# Note: this causes the docker images to be renamed
name: openpipeline
organization: vsh
summary: |
  Best-practice workflows for single-cell multi-omics analyses.
description: |
  OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).

  In terms of workflows, the following has been made available, but keep in mind that
  individual tools and functionality can be executed as standalone components as well.

    * Demultiplexing: conversion of raw sequencing data to FASTQ objects.
    * Ingestion: Read mapping and generating a count matrix.
    * Single sample processing: cell filtering and doublet detection.
    * Multisample processing: Count transformation, normalization, QC metric calulations.
    * Integration: Clustering, integration and batch correction using single and multimodal methods.
    * Downstream analysis workflows
license: MIT
keywords: [single-cell, multimodal]
links:
  repository: https://github.com/openpipelines-bio/openpipeline
  docker_registry: ghcr.io
  homepage: https://openpipelines.bio
  documentation: https://openpipelines.bio/fundamentals
  issue_tracker: https://github.com/openpipelines-bio/openpipeline/issues
info:
  test_resources:
    - type: s3
      path: s3://openpipelines-data
      dest: resources_test
  nextflow_labels_ci:
    - path: src/workflows/utils/labels_ci.config
      description: Adds the correct memory and CPU labels when running on the Viash Hub CI.
config_mods: |
  .resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}
  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'