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

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

Source commit: f9c63d1286

Source message: bump version to v0.1.1
This commit is contained in:
CI
2025-10-02 08:31:47 +00:00
parent 6d0252201f
commit 57d3d9e78b
21 changed files with 144 additions and 86 deletions
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6
CHANGELOG.MD
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@@ -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.

52
README.md Normal file
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@@ -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/).

2
_viash.yaml
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@@ -1,5 +1,5 @@
viash_version: 0.9.4
version: v0.1.0
version: v0.1.1
source: src
target: target
name: openpipeline_qc

10
target/_private/executable/ingestion_qc/h5mu_to_qc_json/.config.vsh.yaml
View File

@@ -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"

14
target/_private/executable/ingestion_qc/h5mu_to_qc_json/h5mu_to_qc_json
View File

@@ -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

10
target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/.config.vsh.yaml
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@@ -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"

14
target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/main.nf
View File

@@ -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",

2
target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/nextflow.config
View File

@@ -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'
}

10
target/executable/ingestion_qc/detect_ingestion_method/.config.vsh.yaml
View File

@@ -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"

14
target/executable/ingestion_qc/detect_ingestion_method/detect_ingestion_method
View File

@@ -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

10
target/executable/ingestion_qc/generate_html/.config.vsh.yaml
View File

@@ -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"

14
target/executable/ingestion_qc/generate_html/generate_html
View File

@@ -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

10
target/nextflow/ingestion_qc/detect_ingestion_method/.config.vsh.yaml
View File

@@ -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"

14
target/nextflow/ingestion_qc/detect_ingestion_method/main.nf
View File

@@ -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",

2
target/nextflow/ingestion_qc/detect_ingestion_method/nextflow.config
View File

@@ -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'
}

10
target/nextflow/ingestion_qc/generate_html/.config.vsh.yaml
View File

@@ -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"

14
target/nextflow/ingestion_qc/generate_html/main.nf
View File

@@ -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",

2
target/nextflow/ingestion_qc/generate_html/nextflow.config
View File

@@ -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'
}

8
target/nextflow/workflows/generate_qc_report/.config.vsh.yaml
View File

@@ -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"

10
target/nextflow/workflows/generate_qc_report/main.nf
View File

@@ -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" : {

2
target/nextflow/workflows/generate_qc_report/nextflow.config
View File

@@ -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'
}