Build branch main with version main (0e87de8)

Build pipeline: viash-hub.htrnaseq.main-29nvl Source commit: 0e87de80bc Source message: Bump craftbox to v0.2.0 (#62)
2025-07-29 11:27:25 +00:00
parent ef4cabdcee
commit 060c9c49a8
104 changed files with 1097 additions and 4230 deletions
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -47,6 +47,9 @@ resources:
 - type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "This component test the ExpressionSet object as output by the main pipeline."
 info: null
 status: "enabled"
@@ -152,9 +155,9 @@ build_info:
  output: "target/executable/integration_test_components/htrnaseq/check_eset"
  executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
  viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
  name: "htrnaseq"
  version: "main"
@@ -185,7 +188,8 @@ package_config:
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main'"
--- a/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml
@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:22Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -54,6 +54,9 @@ resources:
 - type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
+- type: "file"
+  path: "_viash.yaml"
+  dest: "_viash.yaml"
 description: "This component test the cutadapt output from the well_demultiplex subworkflow."
 info: null
 status: "enabled"
@@ -161,9 +164,9 @@ build_info:
  output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
  executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
  viash_version: "0.9.4"
-  git_commit: "a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-6-ga3b7ae3"
+  git_tag: "v0.7.2-9-g0e87de8"
 package_config:
  name: "htrnaseq"
  version: "main"
@@ -194,7 +197,8 @@ package_config:
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
-    \ dest: 'nextflow_labels.config'}\n"
+    \ dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest:\
+    \ '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main'"
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
@@ -0,0 +1,21 @@
+name: htrnaseq
+summary: |
+  A workflow for high-throughput RNA-seq data analyses.
+description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"
+license: MIT
+keywords: [bioinformatics, sequencing, high-throughput, RNAseq, mapping, counting, pipeline, workflow]
+links:
+  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
+  repository: https://github.com/viash-hub/htrnaseq
+viash_version: 0.9.4
+info:
+  test_resources:
+    - path: gs://viash-hub-resources/htrnaseq/v1
+      dest: resources_test
+config_mods: |
+  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .resources += {path: '/_viash.yaml', dest: '_viash.yaml'}
+version: main
+organization: vsh
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
-LABEL org.opencontainers.image.created="2025-07-25T08:01:22Z"
+LABEL org.opencontainers.image.created="2025-07-29T10:37:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a3b7ae3f31ff5eeee305a2cca1ce09ebe1cd8957"
+LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER