diff --git a/CHANGELOG.md b/CHANGELOG.md index 8769792..95dfeeb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# openpipeline_composed 0.1.1 + +## MINOR CHANGES + +* Add a README (PR #4). + # openpipeline_composed 0.1.0 Initial release containing a single-cell meta-workflow to process single cell omics samples, perform batch integration and/or label projection. \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..60eb989 --- /dev/null +++ b/README.md @@ -0,0 +1,42 @@ +# OpenPipeline Composed + +OpenPipeline Composed provides a comprehensive meta-workflow that combines multiple stand-alone workflows from the [OpenPipeline](https://github.com/openpipelines-bio/openpipeline/) package. The meta-workflow combines sample processing, batch integration, and cell type annotation into a unified pipeline for single-cell multi-omics data analysis. + +[![ViashHub](https://img.shields.io/badge/ViashHub-openpipeline_composed-7a4baa.svg)](https://www.viash-hub.com/packages/openpipeline_composed) +[![GitHub](https://img.shields.io/badge/GitHub-openpipelines--bio%2Fopenpipeline_composed-blue.svg)](https://github.com/openpipelines-bio/openpipeline_composed) +[![GitHub License](https://img.shields.io/github/license/openpipelines-bio/openpipeline_composed.svg)](https://github.com/openpipelines-bio/openpipeline_composed/blob/main/LICENSE) +[![GitHub Issues](https://img.shields.io/github/issues/openpipelines-bio/openpipeline_composed.svg)](https://github.com/openpipelines-bio/openpipeline_composed/issues) +[![Viash version](https://img.shields.io/badge/Viash-v0.9.4-blue.svg)](https://viash.io) + +## Overview + +The sole purpose of this package is to provide a meta-workflow that orchestrates and combines various stand-alone workflows from the [OpenPipeline](https://github.com/openpipelines-bio/openpipeline/) package. By integrating multiple processing steps into a single workflow, it enables seamless processing from raw data to fully annotated, integrated datasets suitable for downstream analysis and atlas generation. + +## Functionality + +The meta-workflow combines three core OpenPipeline workflows: +- [**Sample Processing**](https://www.viash-hub.com/packages/openpipeline/latest/components/workflows/multiomics/process_samples): Initial quality control, filtering, and preprocessing +- [**Batch Integration**](https://www.viash-hub.com/packages/openpipeline/latest/components?search=workflows%2Fintegration): Integration using **Harmony** or **scVI** methods +- [**Cell Type Annotation**](https://www.viash-hub.com/packages/openpipeline/latest/components?search=workflows%2Fannotation): Annotation using **scANVI** or **CellTypist** methods + +## Key Features + +- 🔄 **End-to-End Processing**: Complete pipeline from raw data to annotated results +- 📊 **Atlas Generation**: Create comprehensive atlases from multiple datasets and sources +- 🔬 **Multi-Modal Support**: Process RNA-seq, ATAC-seq, protein, and spatial data +- 🎯 **Method Flexibility**: Choose from multiple integration and annotation approaches +- 🧬 **Reference Integration**: Leverage existing reference datasets for annotation + +## Execution via CLI or Seqera Cloud + +The openpipeline_composed package is available via [Viash Hub](https://www.viash-hub.com/packages/openpipeline_composed/latest/), where you can receive instructions on how to run the end-to-end workflow as well as individual subworkflows or components. + +It's possible to run the workflow directly from Seqera Cloud. The necessary Nextflow schema files have been built and provided with the workflows in order to use the form-based input. However, Seqera Cloud can not deal with multiple-value parameters for batch processing of multiple samples. Therefore, it's better to use Viash Hub also here for launching the workflow on Seqera Cloud. + +* Navigate to the [Viash Hub package page](https://www.viash-hub.com/packages/openpipeline_composed/latest/), select the workflow you want to launch and click the `launch` button. +* Select the execution environment of choice (e.g. `Seqera Cloud`, `Nextflow` or `Executable`) +* Fill in the form with the required parameters and launch the workflow. + +## Support + +For issues specific to the composed meta-workflow, please use the [GitHub issues tracker](https://github.com/openpipelines-bio/openpipeline_composed/issues). For general OpenPipeline questions, refer to the main [OpenPipeline documentation](https://openpipelines.bio/). diff --git a/_viash.yaml b/_viash.yaml index 317cded..63f3b0a 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ viash_version: 0.9.4 -version: v0.1.0 +version: v0.1.1 source: src target: target name: openpipeline_composed diff --git a/target/nextflow/single_cell/process_integrate_annotate/.config.vsh.yaml b/target/nextflow/single_cell/process_integrate_annotate/.config.vsh.yaml index 41b8b1f..e9633eb 100644 --- a/target/nextflow/single_cell/process_integrate_annotate/.config.vsh.yaml +++ b/target/nextflow/single_cell/process_integrate_annotate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "process_integrate_annotate" namespace: "single_cell" -version: "v0.1.0" +version: "v0.1.1" authors: - name: "Dorien Roosen" roles: @@ -785,7 +785,7 @@ build_info: output: "target/nextflow/single_cell/process_integrate_annotate" executable: "target/nextflow/single_cell/process_integrate_annotate/main.nf" viash_version: "0.9.4" - git_commit: "7fd732bb4e4fab3fe9d0dde7ad95d13876b60328" + git_commit: "0638f5b2f800a791a266882a3e940cc2f7fc537e" git_remote: "https://github.com/openpipelines-bio/openpipeline_composed" dependencies: - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/multiomics/process_samples" @@ -795,7 +795,7 @@ build_info: - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/integration/scvi_leiden" package_config: name: "openpipeline_composed" - version: "v0.1.0" + version: "v0.1.1" info: test_resources: - type: "s3" @@ -816,7 +816,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" links: repository: "https://github.com/openpipelines-bio/openpipeline_composed" diff --git a/target/nextflow/single_cell/process_integrate_annotate/main.nf b/target/nextflow/single_cell/process_integrate_annotate/main.nf index 7259598..b1ddcf6 100644 --- a/target/nextflow/single_cell/process_integrate_annotate/main.nf +++ b/target/nextflow/single_cell/process_integrate_annotate/main.nf @@ -1,4 +1,4 @@ -// process_integrate_annotate v0.1.0 +// process_integrate_annotate v0.1.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "process_integrate_annotate", "namespace" : "single_cell", - "version" : "v0.1.0", + "version" : "v0.1.1", "authors" : [ { "name" : "Dorien Roosen", @@ -3971,12 +3971,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/single_cell/process_integrate_annotate", "viash_version" : "0.9.4", - "git_commit" : "7fd732bb4e4fab3fe9d0dde7ad95d13876b60328", + "git_commit" : "0638f5b2f800a791a266882a3e940cc2f7fc537e", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_composed" }, "package_config" : { "name" : "openpipeline_composed", - "version" : "v0.1.0", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -4001,7 +4001,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/configs/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh", "links" : { diff --git a/target/nextflow/single_cell/process_integrate_annotate/nextflow.config b/target/nextflow/single_cell/process_integrate_annotate/nextflow.config index be6aba6..07e712f 100644 --- a/target/nextflow/single_cell/process_integrate_annotate/nextflow.config +++ b/target/nextflow/single_cell/process_integrate_annotate/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'single_cell/process_integrate_annotate' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'A pipeline to process, integrate and annotate single cell (multi-)omics data.\nAvailable integration methods:\n- Harmony\n- scVI\nAvailable annotation methods:\n- CellTypist\n- scANVI (with scArches)\n' author = 'Dorien Roosen, Weiwei Schultz' }