Build branch openpipeline_qc/v0.1 with version v0.1.1 to openpipeline_qc on branch v0.1 (f9c63d1)

Build pipeline: openpipelines-bio.openpipeline-qc.0.1.1-976qz

Source commit: f9c63d1286

Source message: bump version to v0.1.1

CHANGELOG.MD

@@ -1,3 +1,9 @@
+# openpipeline_qc 0.1.1
+
+## MINOR CHANGES
+
+* Add a README (PR #9).
+
 # openpipeline_qc 0.1.0
 
 Initial release containing a QC Reporting workflow for Xenium or CellRanger Multi ingested data, with corresponding components.

README.md

@@ -0,0 +1,52 @@
+# OpenPipeline QC
+
+OpenPipeline QC contains an extensible workflow for the generation of a stand-alone, interactive ingestion QC report for single-cell and spatial omics data. It is part of the [OpenPipeline](https://github.com/openpipelines-bio/openpipeline/) ecosystem and extends it with specialized functionality for ingestion quality control.
+
+[![ViashHub](https://img.shields.io/badge/ViashHub-openpipeline_qc-7a4baa.svg)](https://www.viash-hub.com/packages/openpipeline_qc)
+[![GitHub](https://img.shields.io/badge/GitHub-openpipelines--bio%2Fopenpipeline_qc-blue.svg)](https://github.com/openpipelines-bio/openpipeline_qc)
+[![GitHub License](https://img.shields.io/github/license/openpipelines-bio/openpipeline_qc.svg)](https://github.com/openpipelines-bio/openpipeline_qc/blob/main/LICENSE)
+[![GitHub Issues](https://img.shields.io/github/issues/openpipelines-bio/openpipeline_qc.svg)](https://github.com/openpipelines-bio/openpipeline_qc/issues)
+[![Viash version](https://img.shields.io/badge/Viash-v0.9.3-blue.svg)](https://viash.io)
+
+## Functionality
+
+### 1. QC Metrics Calculation
+
+The workflow calculates extensive ingestion QC metrics at both the observation and feature levels. **Observation-level metrics** include total counts per cell, gene detection rates, mitochondrial and ribosomal gene percentages, and expression concentration in top genes. **Feature-level metrics** cover gene expression summaries such as total counts per gene, detection rates across cells, mean expression levels, and dropout percentages.
+
+**Spatial data metrics:**
+For spatial data, the workflow also surfaces segmentation metrics.
+
+### 2. Interactive Report Generation
+
+After calculating QC metrics, the workflow generates a standalone interactive report using the [siqc](https://github.com/openpipelines-bio/siqc) package (standalone, interactive QC reporting engine). 
+
+**siqc features:**
+- 🚀 **Progressive Loading**: Large datasets (millions of cells) load incrementally without blocking the UI
+- 📊 **Interactive Visualizations**: Histograms, scatter plots, heatmaps, and spatial plots with Plotly.js
+- 🗜️ **Efficient Compression**: Binary data format with gzip compression for optimal file sizes
+- 📄 **Standalone Reports**: Single HTML file with no external dependencies
+- 🎯 **Spatial Analysis**: Advanced spatial plotting with faceting and optimization
+- ⚡ **Performance Optimized**: Web Workers, typed arrays, and multi-scale rendering
+
+### 3. Quality Assessment for Downstream Processing
+
+The generated report can be used to set thresholds for QC-based filtering, which can then be applied for further processing of the data using the core [OpenPipeline](https://github.com/openpipelines-bio/openpipeline/) of [OpenPipeline Spatial](https://github.com/openpipelines-bio/openpipeline_spatial/) packages.
+
+**Supported platforms:**
+- 10x Genomics single-cell multi-omics (Cellranger Multi output)
+- 10x Genomics Xenium spatial transcriptomics
+
+## Execution via CLI or Seqera Cloud
+
+The openpipeline_qc package is available via [Viash Hub](https://www.viash-hub.com/packages/openpipeline_qc/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](https://packages.viash-hub.com/vsh/openpipeline_qc/-/tree/build/main/target/nextflow/workflows/generate_qc_report) 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_qc/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 quality control analysis, please use the [GitHub issues tracker](https://github.com/openpipelines-bio/openpipeline_qc/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_qc

target/_private/executable/ingestion_qc/h5mu_to_qc_json/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "h5mu_to_qc_json"
 namespace: "ingestion_qc"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -408,7 +408,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -447,11 +447,11 @@ build_info:
   output: "target/_private/executable/ingestion_qc/h5mu_to_qc_json"
   executable: "target/_private/executable/ingestion_qc/h5mu_to_qc_json/h5mu_to_qc_json"
   viash_version: "0.9.4"
-  git_commit: "32fff3144efcca38eedbd666f52dd3fec369d929"
+  git_commit: "f9c63d1286be56f8be94712d9c1079c1a474ce4d"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
   name: "openpipeline_qc"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -476,7 +476,7 @@ 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_qc"

target/_private/executable/ingestion_qc/h5mu_to_qc_json/h5mu_to_qc_json

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# h5mu_to_qc_json v0.1.0
+# h5mu_to_qc_json 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
@@ -461,10 +461,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik, Dorien Roosen, Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component ingestion_qc h5mu_to_qc_json"
-LABEL org.opencontainers.image.created="2025-09-29T15:35:11Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:17:41Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_qc"
-LABEL org.opencontainers.image.revision="32fff3144efcca38eedbd666f52dd3fec369d929"
+LABEL org.opencontainers.image.revision="f9c63d1286be56f8be94712d9c1079c1a474ce4d"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "h5mu_to_qc_json v0.1.0"
+  echo "h5mu_to_qc_json v0.1.1"
   echo ""
   echo "Takes H5MU files that have been ingested by CellRanger, Xenium or CosMx and"
   echo "processed by the QC workflow, and generates:"
@@ -752,7 +752,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "h5mu_to_qc_json v0.1.0"
+            echo "h5mu_to_qc_json v0.1.1"
             exit
             ;;
         --input)
@@ -1092,7 +1092,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_qc/ingestion_qc/h5mu_to_qc_json:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_qc/ingestion_qc/h5mu_to_qc_json:v0.1.1'
   fi
 
   # print dockerfile

target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "h5mu_to_qc_json"
 namespace: "ingestion_qc"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -408,7 +408,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -447,11 +447,11 @@ build_info:
   output: "target/_private/nextflow/ingestion_qc/h5mu_to_qc_json"
   executable: "target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/main.nf"
   viash_version: "0.9.4"
-  git_commit: "32fff3144efcca38eedbd666f52dd3fec369d929"
+  git_commit: "f9c63d1286be56f8be94712d9c1079c1a474ce4d"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
   name: "openpipeline_qc"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -476,7 +476,7 @@ 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_qc"

target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/main.nf

@@ -1,4 +1,4 @@
-// h5mu_to_qc_json v0.1.0
+// h5mu_to_qc_json 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
@@ -3038,7 +3038,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "h5mu_to_qc_json",
   "namespace" : "ingestion_qc",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3561,7 +3561,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3616,12 +3616,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json",
     "viash_version" : "0.9.4",
-    "git_commit" : "32fff3144efcca38eedbd666f52dd3fec369d929",
+    "git_commit" : "f9c63d1286be56f8be94712d9c1079c1a474ce4d",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_qc"
   },
   "package_config" : {
     "name" : "openpipeline_qc",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3652,7 +3652,7 @@ 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" : {
@@ -4447,7 +4447,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_qc/ingestion_qc/h5mu_to_qc_json",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "midmem",

target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'ingestion_qc/h5mu_to_qc_json'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Takes H5MU files that have been ingested by CellRanger, Xenium or CosMx and processed by the QC workflow, and generates:\n- A JSON file that contains the combined data for the QC report\n- A JSON file that defines the layout and structure of the QC report\n'
   author = 'Jakub Majercik, Dorien Roosen, Robrecht Cannoodt, Weiwei Schultz'
 }

target/executable/ingestion_qc/detect_ingestion_method/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "detect_ingestion_method"
 namespace: "ingestion_qc"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -190,7 +190,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -229,11 +229,11 @@ build_info:
   output: "target/executable/ingestion_qc/detect_ingestion_method"
   executable: "target/executable/ingestion_qc/detect_ingestion_method/detect_ingestion_method"
   viash_version: "0.9.4"
-  git_commit: "32fff3144efcca38eedbd666f52dd3fec369d929"
+  git_commit: "f9c63d1286be56f8be94712d9c1079c1a474ce4d"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
   name: "openpipeline_qc"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -258,7 +258,7 @@ 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_qc"

target/executable/ingestion_qc/detect_ingestion_method/detect_ingestion_method

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# detect_ingestion_method v0.1.0
+# detect_ingestion_method 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
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component ingestion_qc detect_ingestion_method"
-LABEL org.opencontainers.image.created="2025-09-29T15:35:11Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:17:41Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_qc"
-LABEL org.opencontainers.image.revision="32fff3144efcca38eedbd666f52dd3fec369d929"
+LABEL org.opencontainers.image.revision="f9c63d1286be56f8be94712d9c1079c1a474ce4d"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "detect_ingestion_method v0.1.0"
+  echo "detect_ingestion_method v0.1.1"
   echo ""
   echo "Detects the ingestion method of a dataset."
   echo "Currently detects either 10X CellRanger Multi, 10X Xenium or Nanostring CosMx,"
@@ -656,7 +656,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "detect_ingestion_method v0.1.0"
+            echo "detect_ingestion_method v0.1.1"
             exit
             ;;
         --input)
@@ -791,7 +791,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_qc/ingestion_qc/detect_ingestion_method:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_qc/ingestion_qc/detect_ingestion_method:v0.1.1'
   fi
 
   # print dockerfile

target/executable/ingestion_qc/generate_html/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_html"
 namespace: "ingestion_qc"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -209,7 +209,7 @@ engines:
   id: "docker"
   image: "node:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -231,11 +231,11 @@ build_info:
   output: "target/executable/ingestion_qc/generate_html"
   executable: "target/executable/ingestion_qc/generate_html/generate_html"
   viash_version: "0.9.4"
-  git_commit: "32fff3144efcca38eedbd666f52dd3fec369d929"
+  git_commit: "f9c63d1286be56f8be94712d9c1079c1a474ce4d"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
   name: "openpipeline_qc"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -260,7 +260,7 @@ 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_qc"

target/executable/ingestion_qc/generate_html/generate_html

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# generate_html v0.1.0
+# generate_html 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
@@ -462,10 +462,10 @@ RUN npm install -g pnpm@latest-10 \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik, Dorien Roosen, Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component ingestion_qc generate_html"
-LABEL org.opencontainers.image.created="2025-09-29T15:35:11Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:17:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_qc"
-LABEL org.opencontainers.image.revision="32fff3144efcca38eedbd666f52dd3fec369d929"
+LABEL org.opencontainers.image.revision="f9c63d1286be56f8be94712d9c1079c1a474ce4d"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -582,7 +582,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "generate_html v0.1.0"
+  echo "generate_html v0.1.1"
   echo ""
   echo "Generate an HTML report from the QC metrics"
   echo ""
@@ -650,7 +650,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "generate_html v0.1.0"
+            echo "generate_html v0.1.1"
             exit
             ;;
         --input_data)
@@ -774,7 +774,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_qc/ingestion_qc/generate_html:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_qc/ingestion_qc/generate_html:v0.1.1'
   fi
 
   # print dockerfile

target/nextflow/ingestion_qc/detect_ingestion_method/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "detect_ingestion_method"
 namespace: "ingestion_qc"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -190,7 +190,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -229,11 +229,11 @@ build_info:
   output: "target/nextflow/ingestion_qc/detect_ingestion_method"
   executable: "target/nextflow/ingestion_qc/detect_ingestion_method/main.nf"
   viash_version: "0.9.4"
-  git_commit: "32fff3144efcca38eedbd666f52dd3fec369d929"
+  git_commit: "f9c63d1286be56f8be94712d9c1079c1a474ce4d"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
   name: "openpipeline_qc"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -258,7 +258,7 @@ 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_qc"

target/nextflow/ingestion_qc/detect_ingestion_method/main.nf

@@ -1,4 +1,4 @@
-// detect_ingestion_method v0.1.0
+// detect_ingestion_method 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" : "detect_ingestion_method",
   "namespace" : "ingestion_qc",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3290,7 +3290,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3345,12 +3345,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/ingestion_qc/detect_ingestion_method",
     "viash_version" : "0.9.4",
-    "git_commit" : "32fff3144efcca38eedbd666f52dd3fec369d929",
+    "git_commit" : "f9c63d1286be56f8be94712d9c1079c1a474ce4d",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_qc"
   },
   "package_config" : {
     "name" : "openpipeline_qc",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3381,7 +3381,7 @@ 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" : {
@@ -3872,7 +3872,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_qc/ingestion_qc/detect_ingestion_method",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "lowmem",

target/nextflow/ingestion_qc/detect_ingestion_method/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'ingestion_qc/detect_ingestion_method'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Detects the ingestion method of a dataset.\nCurrently detects either 10X CellRanger Multi, 10X Xenium or Nanostring CosMx, but can be extended to other technologies upon request.\n'
   author = 'Dorien Roosen, Weiwei Schultz'
 }

target/nextflow/ingestion_qc/generate_html/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_html"
 namespace: "ingestion_qc"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -209,7 +209,7 @@ engines:
   id: "docker"
   image: "node:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -231,11 +231,11 @@ build_info:
   output: "target/nextflow/ingestion_qc/generate_html"
   executable: "target/nextflow/ingestion_qc/generate_html/main.nf"
   viash_version: "0.9.4"
-  git_commit: "32fff3144efcca38eedbd666f52dd3fec369d929"
+  git_commit: "f9c63d1286be56f8be94712d9c1079c1a474ce4d"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
   name: "openpipeline_qc"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -260,7 +260,7 @@ 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_qc"

target/nextflow/ingestion_qc/generate_html/main.nf

@@ -1,4 +1,4 @@
-// generate_html v0.1.0
+// generate_html 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
@@ -3038,7 +3038,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "generate_html",
   "namespace" : "ingestion_qc",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3330,7 +3330,7 @@ meta = [
       "id" : "docker",
       "image" : "node:latest",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3359,12 +3359,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/ingestion_qc/generate_html",
     "viash_version" : "0.9.4",
-    "git_commit" : "32fff3144efcca38eedbd666f52dd3fec369d929",
+    "git_commit" : "f9c63d1286be56f8be94712d9c1079c1a474ce4d",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_qc"
   },
   "package_config" : {
     "name" : "openpipeline_qc",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3395,7 +3395,7 @@ 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" : {
@@ -3840,7 +3840,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_qc/ingestion_qc/generate_html",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "lowmem",

target/nextflow/ingestion_qc/generate_html/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'ingestion_qc/generate_html'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Generate an HTML report from the QC metrics'
   author = 'Jakub Majercik, Dorien Roosen, Robrecht Cannoodt, Weiwei Schultz'
 }

target/nextflow/workflows/generate_qc_report/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_qc_report"
 namespace: "workflows"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -375,7 +375,7 @@ build_info:
   output: "target/nextflow/workflows/generate_qc_report"
   executable: "target/nextflow/workflows/generate_qc_report/main.nf"
   viash_version: "0.9.4"
-  git_commit: "32fff3144efcca38eedbd666f52dd3fec369d929"
+  git_commit: "f9c63d1286be56f8be94712d9c1079c1a474ce4d"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
   dependencies:
   - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/metadata/add_id"
@@ -386,7 +386,7 @@ build_info:
   - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory"
 package_config:
   name: "openpipeline_qc"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -411,7 +411,7 @@ 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_qc"

target/nextflow/workflows/generate_qc_report/main.nf

@@ -1,4 +1,4 @@
-// generate_qc_report v0.1.0
+// generate_qc_report 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
@@ -3038,7 +3038,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "generate_qc_report",
   "namespace" : "workflows",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3532,12 +3532,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/generate_qc_report",
     "viash_version" : "0.9.4",
-    "git_commit" : "32fff3144efcca38eedbd666f52dd3fec369d929",
+    "git_commit" : "f9c63d1286be56f8be94712d9c1079c1a474ce4d",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_qc"
   },
   "package_config" : {
     "name" : "openpipeline_qc",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3568,7 +3568,7 @@ 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/workflows/generate_qc_report/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/generate_qc_report'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Run the ingestion QC report generation'
   author = 'Jakub Majercik, Dorien Roosen, Robrecht Cannoodt, Weiwei Schultz'
 }