Build branch build/main with version build_main (31245d8)

Build pipeline: openpipelines-bio.openpipeline-qc.build-main-km8q4 Source commit: 31245d83cd Source message: deploy: 4b5539227ceaa6be5c7e97ca45fcf3aa025466fd
2025-08-12 14:44:58 +00:00
parent 48e69ee3fa
commit b8ac2db1ac
16 changed files with 64 additions and 61 deletions
--- a/CHANGELOG.MD
+++ b/CHANGELOG.MD
@@ -0,0 +1,3 @@
+# openpipeline_qc x.x.x
+
+Initial release containing a QC Reporting workflow for Xenium or CellRanger Multi ingested data, with corresponding components.
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,10 +1,10 @@
 viash_version: 0.9.4
 source: src
 target: target
-name: openpipeline_incubator
+name: openpipeline_qc
 organization: openpipelines-bio
 links:
-  repository: https://github.com/openpipelines-bio/openpipeline_incubator
+  repository: https://github.com/openpipelines-bio/openpipeline_qc
  docker_registry: ghcr.io
 repositories:
  - name: openpipeline
--- 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
@@ -331,7 +331,7 @@ repositories:
  repo: "craftbox"
  tag: "v0.2.0"
 links:
-  repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+  repository: "https://github.com/openpipelines-bio/openpipeline_qc"
  docker_registry: "ghcr.io"
 runners:
 - type: "executable"
@@ -447,10 +447,10 @@ 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: "dfd68e55fafa27fc489f14bfab8ad04315f7f233"
+  git_commit: "31245d83cd69ca747cb4610bed18692a3a3914f0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
-  name: "openpipeline_incubator"
+  name: "openpipeline_qc"
  version: "build_main"
  info:
    test_resources:
@@ -479,5 +479,5 @@ package_config:
  - ".engines[.type == 'docker'].target_tag := 'build_main'"
  organization: "vsh"
  links:
-    repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+    repository: "https://github.com/openpipelines-bio/openpipeline_qc"
    docker_registry: "ghcr.io"
--- 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
@@ -461,9 +461,9 @@ 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="2025-08-11T08:32:06Z"
-LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_incubator"
-LABEL org.opencontainers.image.revision="dfd68e55fafa27fc489f14bfab8ad04315f7f233"
+LABEL org.opencontainers.image.created="2025-08-12T14:28:42Z"
+LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_qc"
+LABEL org.opencontainers.image.revision="31245d83cd69ca747cb4610bed18692a3a3914f0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
@@ -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_incubator/ingestion_qc/h5mu_to_qc_json:build_main'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_qc/ingestion_qc/h5mu_to_qc_json:build_main'
  fi

  # print dockerfile
--- 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
@@ -331,7 +331,7 @@ repositories:
  repo: "craftbox"
  tag: "v0.2.0"
 links:
-  repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+  repository: "https://github.com/openpipelines-bio/openpipeline_qc"
  docker_registry: "ghcr.io"
 runners:
 - type: "executable"
@@ -447,10 +447,10 @@ 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: "dfd68e55fafa27fc489f14bfab8ad04315f7f233"
+  git_commit: "31245d83cd69ca747cb4610bed18692a3a3914f0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
-  name: "openpipeline_incubator"
+  name: "openpipeline_qc"
  version: "build_main"
  info:
    test_resources:
@@ -479,5 +479,5 @@ package_config:
  - ".engines[.type == 'docker'].target_tag := 'build_main'"
  organization: "vsh"
  links:
-    repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+    repository: "https://github.com/openpipelines-bio/openpipeline_qc"
    docker_registry: "ghcr.io"
--- a/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/main.nf
+++ b/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json/main.nf
@@ -3471,7 +3471,7 @@ meta = [
    }
  ],
  "links" : {
-    "repository" : "https://github.com/openpipelines-bio/openpipeline_incubator",
+    "repository" : "https://github.com/openpipelines-bio/openpipeline_qc",
    "docker_registry" : "ghcr.io"
  },
  "runners" : [
@@ -3616,11 +3616,11 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/_private/nextflow/ingestion_qc/h5mu_to_qc_json",
    "viash_version" : "0.9.4",
-    "git_commit" : "dfd68e55fafa27fc489f14bfab8ad04315f7f233",
+    "git_commit" : "31245d83cd69ca747cb4610bed18692a3a3914f0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_qc"
  },
  "package_config" : {
-    "name" : "openpipeline_incubator",
+    "name" : "openpipeline_qc",
    "version" : "build_main",
    "info" : {
      "test_resources" : [
@@ -3656,7 +3656,7 @@ meta = [
    ],
    "organization" : "vsh",
    "links" : {
-      "repository" : "https://github.com/openpipelines-bio/openpipeline_incubator",
+      "repository" : "https://github.com/openpipelines-bio/openpipeline_qc",
      "docker_registry" : "ghcr.io"
    }
  }
@@ -4446,7 +4446,7 @@ meta["defaults"] = [
  directives: readJsonBlob('''{
  "container" : {
    "registry" : "images.viash-hub.com",
-    "image" : "vsh/openpipeline_incubator/ingestion_qc/h5mu_to_qc_json",
+    "image" : "vsh/openpipeline_qc/ingestion_qc/h5mu_to_qc_json",
    "tag" : "build_main"
  },
  "label" : [
--- a/target/executable/ingestion_qc/detect_ingestion_method/.config.vsh.yaml
+++ b/target/executable/ingestion_qc/detect_ingestion_method/.config.vsh.yaml
@@ -113,7 +113,7 @@ repositories:
  repo: "craftbox"
  tag: "v0.2.0"
 links:
-  repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+  repository: "https://github.com/openpipelines-bio/openpipeline_qc"
  docker_registry: "ghcr.io"
 runners:
 - type: "executable"
@@ -229,10 +229,10 @@ 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: "dfd68e55fafa27fc489f14bfab8ad04315f7f233"
+  git_commit: "31245d83cd69ca747cb4610bed18692a3a3914f0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
-  name: "openpipeline_incubator"
+  name: "openpipeline_qc"
  version: "build_main"
  info:
    test_resources:
@@ -261,5 +261,5 @@ package_config:
  - ".engines[.type == 'docker'].target_tag := 'build_main'"
  organization: "vsh"
  links:
-    repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+    repository: "https://github.com/openpipelines-bio/openpipeline_qc"
    docker_registry: "ghcr.io"
--- a/target/executable/ingestion_qc/detect_ingestion_method/detect_ingestion_method
+++ b/target/executable/ingestion_qc/detect_ingestion_method/detect_ingestion_method
@@ -459,9 +459,9 @@ 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="2025-08-11T08:32:06Z"
-LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_incubator"
-LABEL org.opencontainers.image.revision="dfd68e55fafa27fc489f14bfab8ad04315f7f233"
+LABEL org.opencontainers.image.created="2025-08-12T14:28:42Z"
+LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_qc"
+LABEL org.opencontainers.image.revision="31245d83cd69ca747cb4610bed18692a3a3914f0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
@@ -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_incubator/ingestion_qc/detect_ingestion_method:build_main'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_qc/ingestion_qc/detect_ingestion_method:build_main'
  fi

  # print dockerfile
--- a/target/executable/ingestion_qc/generate_html/.config.vsh.yaml
+++ b/target/executable/ingestion_qc/generate_html/.config.vsh.yaml
@@ -132,7 +132,7 @@ repositories:
  repo: "craftbox"
  tag: "v0.2.0"
 links:
-  repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+  repository: "https://github.com/openpipelines-bio/openpipeline_qc"
  docker_registry: "ghcr.io"
 runners:
 - type: "executable"
@@ -231,10 +231,10 @@ 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: "dfd68e55fafa27fc489f14bfab8ad04315f7f233"
+  git_commit: "31245d83cd69ca747cb4610bed18692a3a3914f0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
-  name: "openpipeline_incubator"
+  name: "openpipeline_qc"
  version: "build_main"
  info:
    test_resources:
@@ -263,5 +263,5 @@ package_config:
  - ".engines[.type == 'docker'].target_tag := 'build_main'"
  organization: "vsh"
  links:
-    repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+    repository: "https://github.com/openpipelines-bio/openpipeline_qc"
    docker_registry: "ghcr.io"
--- a/target/executable/ingestion_qc/generate_html/generate_html
+++ b/target/executable/ingestion_qc/generate_html/generate_html
@@ -462,9 +462,9 @@ 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="2025-08-11T08:32:06Z"
-LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_incubator"
-LABEL org.opencontainers.image.revision="dfd68e55fafa27fc489f14bfab8ad04315f7f233"
+LABEL org.opencontainers.image.created="2025-08-12T14:28:42Z"
+LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_qc"
+LABEL org.opencontainers.image.revision="31245d83cd69ca747cb4610bed18692a3a3914f0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
@@ -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_incubator/ingestion_qc/generate_html:build_main'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_qc/ingestion_qc/generate_html:build_main'
  fi

  # print dockerfile
--- a/target/nextflow/ingestion_qc/detect_ingestion_method/.config.vsh.yaml
+++ b/target/nextflow/ingestion_qc/detect_ingestion_method/.config.vsh.yaml
@@ -113,7 +113,7 @@ repositories:
  repo: "craftbox"
  tag: "v0.2.0"
 links:
-  repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+  repository: "https://github.com/openpipelines-bio/openpipeline_qc"
  docker_registry: "ghcr.io"
 runners:
 - type: "executable"
@@ -229,10 +229,10 @@ 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: "dfd68e55fafa27fc489f14bfab8ad04315f7f233"
+  git_commit: "31245d83cd69ca747cb4610bed18692a3a3914f0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
-  name: "openpipeline_incubator"
+  name: "openpipeline_qc"
  version: "build_main"
  info:
    test_resources:
@@ -261,5 +261,5 @@ package_config:
  - ".engines[.type == 'docker'].target_tag := 'build_main'"
  organization: "vsh"
  links:
-    repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+    repository: "https://github.com/openpipelines-bio/openpipeline_qc"
    docker_registry: "ghcr.io"
--- a/target/nextflow/ingestion_qc/detect_ingestion_method/main.nf
+++ b/target/nextflow/ingestion_qc/detect_ingestion_method/main.nf
@@ -3200,7 +3200,7 @@ meta = [
    }
  ],
  "links" : {
-    "repository" : "https://github.com/openpipelines-bio/openpipeline_incubator",
+    "repository" : "https://github.com/openpipelines-bio/openpipeline_qc",
    "docker_registry" : "ghcr.io"
  },
  "runners" : [
@@ -3345,11 +3345,11 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/ingestion_qc/detect_ingestion_method",
    "viash_version" : "0.9.4",
-    "git_commit" : "dfd68e55fafa27fc489f14bfab8ad04315f7f233",
+    "git_commit" : "31245d83cd69ca747cb4610bed18692a3a3914f0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_qc"
  },
  "package_config" : {
-    "name" : "openpipeline_incubator",
+    "name" : "openpipeline_qc",
    "version" : "build_main",
    "info" : {
      "test_resources" : [
@@ -3385,7 +3385,7 @@ meta = [
    ],
    "organization" : "vsh",
    "links" : {
-      "repository" : "https://github.com/openpipelines-bio/openpipeline_incubator",
+      "repository" : "https://github.com/openpipelines-bio/openpipeline_qc",
      "docker_registry" : "ghcr.io"
    }
  }
@@ -3871,7 +3871,7 @@ meta["defaults"] = [
  directives: readJsonBlob('''{
  "container" : {
    "registry" : "images.viash-hub.com",
-    "image" : "vsh/openpipeline_incubator/ingestion_qc/detect_ingestion_method",
+    "image" : "vsh/openpipeline_qc/ingestion_qc/detect_ingestion_method",
    "tag" : "build_main"
  },
  "label" : [
--- a/target/nextflow/ingestion_qc/generate_html/.config.vsh.yaml
+++ b/target/nextflow/ingestion_qc/generate_html/.config.vsh.yaml
@@ -132,7 +132,7 @@ repositories:
  repo: "craftbox"
  tag: "v0.2.0"
 links:
-  repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+  repository: "https://github.com/openpipelines-bio/openpipeline_qc"
  docker_registry: "ghcr.io"
 runners:
 - type: "executable"
@@ -231,10 +231,10 @@ 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: "dfd68e55fafa27fc489f14bfab8ad04315f7f233"
+  git_commit: "31245d83cd69ca747cb4610bed18692a3a3914f0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
 package_config:
-  name: "openpipeline_incubator"
+  name: "openpipeline_qc"
  version: "build_main"
  info:
    test_resources:
@@ -263,5 +263,5 @@ package_config:
  - ".engines[.type == 'docker'].target_tag := 'build_main'"
  organization: "vsh"
  links:
-    repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+    repository: "https://github.com/openpipelines-bio/openpipeline_qc"
    docker_registry: "ghcr.io"
--- a/target/nextflow/ingestion_qc/generate_html/main.nf
+++ b/target/nextflow/ingestion_qc/generate_html/main.nf
@@ -3240,7 +3240,7 @@ meta = [
    }
  ],
  "links" : {
-    "repository" : "https://github.com/openpipelines-bio/openpipeline_incubator",
+    "repository" : "https://github.com/openpipelines-bio/openpipeline_qc",
    "docker_registry" : "ghcr.io"
  },
  "runners" : [
@@ -3359,11 +3359,11 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/ingestion_qc/generate_html",
    "viash_version" : "0.9.4",
-    "git_commit" : "dfd68e55fafa27fc489f14bfab8ad04315f7f233",
+    "git_commit" : "31245d83cd69ca747cb4610bed18692a3a3914f0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_qc"
  },
  "package_config" : {
-    "name" : "openpipeline_incubator",
+    "name" : "openpipeline_qc",
    "version" : "build_main",
    "info" : {
      "test_resources" : [
@@ -3399,7 +3399,7 @@ meta = [
    ],
    "organization" : "vsh",
    "links" : {
-      "repository" : "https://github.com/openpipelines-bio/openpipeline_incubator",
+      "repository" : "https://github.com/openpipelines-bio/openpipeline_qc",
      "docker_registry" : "ghcr.io"
    }
  }
@@ -3839,7 +3839,7 @@ meta["defaults"] = [
  directives: readJsonBlob('''{
  "container" : {
    "registry" : "images.viash-hub.com",
-    "image" : "vsh/openpipeline_incubator/ingestion_qc/generate_html",
+    "image" : "vsh/openpipeline_qc/ingestion_qc/generate_html",
    "tag" : "build_main"
  },
  "label" : [
--- a/target/nextflow/workflows/generate_qc_report/.config.vsh.yaml
+++ b/target/nextflow/workflows/generate_qc_report/.config.vsh.yaml
@@ -276,7 +276,7 @@ repositories:
  repo: "craftbox"
  tag: "v0.2.0"
 links:
-  repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+  repository: "https://github.com/openpipelines-bio/openpipeline_qc"
  docker_registry: "ghcr.io"
 runners:
 - type: "nextflow"
@@ -352,7 +352,7 @@ 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: "dfd68e55fafa27fc489f14bfab8ad04315f7f233"
+  git_commit: "31245d83cd69ca747cb4610bed18692a3a3914f0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
  dependencies:
  - "target/dependencies/github/openpipelines-bio/openpipeline/2.1.2/nextflow/metadata/add_id"
@@ -362,7 +362,7 @@ build_info:
  - "target/nextflow/ingestion_qc/generate_html"
  - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory"
 package_config:
-  name: "openpipeline_incubator"
+  name: "openpipeline_qc"
  version: "build_main"
  info:
    test_resources:
@@ -391,5 +391,5 @@ package_config:
  - ".engines[.type == 'docker'].target_tag := 'build_main'"
  organization: "vsh"
  links:
-    repository: "https://github.com/openpipelines-bio/openpipeline_incubator"
+    repository: "https://github.com/openpipelines-bio/openpipeline_qc"
    docker_registry: "ghcr.io"
--- a/target/nextflow/workflows/generate_qc_report/main.nf
+++ b/target/nextflow/workflows/generate_qc_report/main.nf
@@ -3419,7 +3419,7 @@ meta = [
    }
  ],
  "links" : {
-    "repository" : "https://github.com/openpipelines-bio/openpipeline_incubator",
+    "repository" : "https://github.com/openpipelines-bio/openpipeline_qc",
    "docker_registry" : "ghcr.io"
  },
  "runners" : [
@@ -3506,11 +3506,11 @@ meta = [
    "engine" : "native",
    "output" : "/workdir/root/repo/target/nextflow/workflows/generate_qc_report",
    "viash_version" : "0.9.4",
-    "git_commit" : "dfd68e55fafa27fc489f14bfab8ad04315f7f233",
+    "git_commit" : "31245d83cd69ca747cb4610bed18692a3a3914f0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_qc"
  },
  "package_config" : {
-    "name" : "openpipeline_incubator",
+    "name" : "openpipeline_qc",
    "version" : "build_main",
    "info" : {
      "test_resources" : [
@@ -3546,7 +3546,7 @@ meta = [
    ],
    "organization" : "vsh",
    "links" : {
-      "repository" : "https://github.com/openpipelines-bio/openpipeline_incubator",
+      "repository" : "https://github.com/openpipelines-bio/openpipeline_qc",
      "docker_registry" : "ghcr.io"
    }
  }