From 57d3d9e78be8b192ec9731c9d54fc4ea1e75c1e3 Mon Sep 17 00:00:00 2001 From: CI Date: Thu, 2 Oct 2025 08:31:47 +0000 Subject: [PATCH] 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: https://github.com/openpipelines-bio/openpipeline_qc/commit/f9c63d1286be56f8be94712d9c1079c1a474ce4d Source message: bump version to v0.1.1 --- CHANGELOG.MD | 6 +++ README.md | 52 +++++++++++++++++++ _viash.yaml | 2 +- .../h5mu_to_qc_json/.config.vsh.yaml | 10 ++-- .../h5mu_to_qc_json/h5mu_to_qc_json | 14 ++--- .../h5mu_to_qc_json/.config.vsh.yaml | 10 ++-- .../ingestion_qc/h5mu_to_qc_json/main.nf | 14 ++--- .../h5mu_to_qc_json/nextflow.config | 2 +- .../detect_ingestion_method/.config.vsh.yaml | 10 ++-- .../detect_ingestion_method | 14 ++--- .../generate_html/.config.vsh.yaml | 10 ++-- .../ingestion_qc/generate_html/generate_html | 14 ++--- .../detect_ingestion_method/.config.vsh.yaml | 10 ++-- .../detect_ingestion_method/main.nf | 14 ++--- .../detect_ingestion_method/nextflow.config | 2 +- .../generate_html/.config.vsh.yaml | 10 ++-- .../ingestion_qc/generate_html/main.nf | 14 ++--- .../generate_html/nextflow.config | 2 +- .../generate_qc_report/.config.vsh.yaml | 8 +-- .../workflows/generate_qc_report/main.nf | 10 ++-- .../generate_qc_report/nextflow.config | 2 +- 21 files changed, 144 insertions(+), 86 deletions(-) create mode 100644 README.md diff --git a/CHANGELOG.MD b/CHANGELOG.MD index 0470189..70e222f 100644 --- a/CHANGELOG.MD +++ b/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. \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..c35747c --- /dev/null +++ b/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/). diff --git a/_viash.yaml b/_viash.yaml index c3178c4..f965a47 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_qc diff --git a/target/_private/executable/ingestion_qc/h5mu_to_qc_json/.config.vsh.yaml b/target/_private/executable/ingestion_qc/h5mu_to_qc_json/.config.vsh.yaml index bbfc648..9ec1eb1 100644 --- a/target/_private/executable/ingestion_qc/h5mu_to_qc_json/.config.vsh.yaml +++ b/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" diff --git a/target/_private/executable/ingestion_qc/h5mu_to_qc_json/h5mu_to_qc_json b/target/_private/executable/ingestion_qc/h5mu_to_qc_json/h5mu_to_qc_json index f2be70f..243cfbd 100755 --- a/target/_private/executable/ingestion_qc/h5mu_to_qc_json/h5mu_to_qc_json +++ b/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.version="v0.1.0" +LABEL org.opencontainers.image.revision="f9c63d1286be56f8be94712d9c1079c1a474ce4d" +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 diff --git a/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/.config.vsh.yaml b/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/.config.vsh.yaml index ca30a12..6c3b54e 100644 --- a/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/.config.vsh.yaml +++ b/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" diff --git a/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/main.nf b/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/main.nf index 08be2d6..0e7f8a2 100644 --- a/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/main.nf +++ b/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", diff --git a/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/nextflow.config b/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/nextflow.config index 77a388a..18e3105 100644 --- a/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/nextflow.config +++ b/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' } diff --git a/target/executable/ingestion_qc/detect_ingestion_method/.config.vsh.yaml b/target/executable/ingestion_qc/detect_ingestion_method/.config.vsh.yaml index d44c24e..a2b3abe 100644 --- a/target/executable/ingestion_qc/detect_ingestion_method/.config.vsh.yaml +++ b/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" diff --git a/target/executable/ingestion_qc/detect_ingestion_method/detect_ingestion_method b/target/executable/ingestion_qc/detect_ingestion_method/detect_ingestion_method index 899bd6a..bb16bb4 100755 --- a/target/executable/ingestion_qc/detect_ingestion_method/detect_ingestion_method +++ b/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.version="v0.1.0" +LABEL org.opencontainers.image.revision="f9c63d1286be56f8be94712d9c1079c1a474ce4d" +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 diff --git a/target/executable/ingestion_qc/generate_html/.config.vsh.yaml b/target/executable/ingestion_qc/generate_html/.config.vsh.yaml index d8e991e..13e4b2c 100644 --- a/target/executable/ingestion_qc/generate_html/.config.vsh.yaml +++ b/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" diff --git a/target/executable/ingestion_qc/generate_html/generate_html b/target/executable/ingestion_qc/generate_html/generate_html index dac797e..db61fd1 100755 --- a/target/executable/ingestion_qc/generate_html/generate_html +++ b/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.version="v0.1.0" +LABEL org.opencontainers.image.revision="f9c63d1286be56f8be94712d9c1079c1a474ce4d" +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 diff --git a/target/nextflow/ingestion_qc/detect_ingestion_method/.config.vsh.yaml b/target/nextflow/ingestion_qc/detect_ingestion_method/.config.vsh.yaml index 30b4a46..f0af513 100644 --- a/target/nextflow/ingestion_qc/detect_ingestion_method/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/ingestion_qc/detect_ingestion_method/main.nf b/target/nextflow/ingestion_qc/detect_ingestion_method/main.nf index 4add368..2d317ad 100644 --- a/target/nextflow/ingestion_qc/detect_ingestion_method/main.nf +++ b/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", diff --git a/target/nextflow/ingestion_qc/detect_ingestion_method/nextflow.config b/target/nextflow/ingestion_qc/detect_ingestion_method/nextflow.config index 7537911..96eff4c 100644 --- a/target/nextflow/ingestion_qc/detect_ingestion_method/nextflow.config +++ b/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' } diff --git a/target/nextflow/ingestion_qc/generate_html/.config.vsh.yaml b/target/nextflow/ingestion_qc/generate_html/.config.vsh.yaml index f031f6a..804a332 100644 --- a/target/nextflow/ingestion_qc/generate_html/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/ingestion_qc/generate_html/main.nf b/target/nextflow/ingestion_qc/generate_html/main.nf index 372c13c..3133b7e 100644 --- a/target/nextflow/ingestion_qc/generate_html/main.nf +++ b/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", diff --git a/target/nextflow/ingestion_qc/generate_html/nextflow.config b/target/nextflow/ingestion_qc/generate_html/nextflow.config index 9215312..c5874fd 100644 --- a/target/nextflow/ingestion_qc/generate_html/nextflow.config +++ b/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' } diff --git a/target/nextflow/workflows/generate_qc_report/.config.vsh.yaml b/target/nextflow/workflows/generate_qc_report/.config.vsh.yaml index ddb9c77..3cf6cf8 100644 --- a/target/nextflow/workflows/generate_qc_report/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/workflows/generate_qc_report/main.nf b/target/nextflow/workflows/generate_qc_report/main.nf index 4bf0cfe..c7f7bd0 100644 --- a/target/nextflow/workflows/generate_qc_report/main.nf +++ b/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" : { diff --git a/target/nextflow/workflows/generate_qc_report/nextflow.config b/target/nextflow/workflows/generate_qc_report/nextflow.config index b8b3666..5d4964d 100644 --- a/target/nextflow/workflows/generate_qc_report/nextflow.config +++ b/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' }