Build branch openpipeline_composed/v0.1 with version v0.1.1 to openpipeline_composed on branch v0.1 (0638f5b)

Build pipeline: openpipelines-bio.openpipeline-composed.0.1.1-pcdzw

Source commit: 0638f5b2f8

Source message: bump version to v0.1.1

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.

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/).

_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

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"

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" : {

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'
 }