Build branch save-params with version save-params (05ac6a3)

Build pipeline: viash-hub.htrnaseq.save-params-h88fh

Source commit: 05ac6a3d24

Source message: updated filepathpath parsing

target/executable/report/create_report/.config.vsh.yaml

@@ -75,6 +75,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -184,12 +187,14 @@ engines:
     - "install.packages(\"oaStyle\", repos = c(rdepot = \"https://repos.openanalytics.eu/repo/public\"\
       , getOption(\"repos\")))"
     bioc_force_install: false
+    warnings_as_errors: true
   test_setup:
   - type: "r"
     packages:
     - "testthat"
     - "R.utils"
     bioc_force_install: false
+    warnings_as_errors: true
   entrypoint: []
   cmd: null
 - type: "native"
@@ -200,8 +205,8 @@ build_info:
   engine: "docker|native"
   output: "target/executable/report/create_report"
   executable: "target/executable/report/create_report/create_report"
-  viash_version: "0.9.0"
-  git_commit: "1561d769c65192a820053a565654dee8cbe55588"
+  viash_version: "0.9.2"
+  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
@@ -211,7 +216,7 @@ package_config:
     test_resources:
     - path: "gs://viash-hub-test-data/htrnaseq/v1/"
       dest: "resources_test"
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:

target/executable/report/create_report/create_report

@@ -2,7 +2,7 @@
 
 # create_report save-params
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -173,20 +173,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "create_report save-params"
-  echo ""
-  echo "Create a basic QC report in HTML format based on a number of esets."
-  echo ""
-  echo "Arguments:"
-  echo "    --eset"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo ""
-  echo "    --output_report"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: report.html"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -467,18 +453,18 @@ RUN apt-get update && \
   DEBIAN_FRONTEND=noninteractive apt-get install -y procps pandoc && \
   rm -rf /var/lib/apt/lists/*
 
-RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
-  Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
-  Rscript -e 'if (!requireNamespace("Biobase", quietly = TRUE)) BiocManager::install("Biobase")' && \
-  Rscript -e 'if (!requireNamespace("ComplexHeatmap", quietly = TRUE)) BiocManager::install("ComplexHeatmap")' && \
-  Rscript -e 'remotes::install_cran(c("ggplot2", "knitr", "gridExtra", "RColorBrewer", "processx", "whisker", "rmarkdown", "bookdown", "data.table", "platetools", "htmltools", "DT", "logger", "bit64"), repos = "https://cran.rstudio.com")' && \
-  Rscript -e 'install.packages("oaStyle", repos = c(rdepot = "https://repos.openanalytics.eu/repo/public", getOption("repos")))'
+RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
+  Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
+  Rscript -e 'options(warn = 2); if (!requireNamespace("Biobase", quietly = TRUE)) BiocManager::install("Biobase")' && \
+  Rscript -e 'options(warn = 2); if (!requireNamespace("ComplexHeatmap", quietly = TRUE)) BiocManager::install("ComplexHeatmap")' && \
+  Rscript -e 'options(warn = 2); remotes::install_cran(c("ggplot2", "knitr", "gridExtra", "RColorBrewer", "processx", "whisker", "rmarkdown", "bookdown", "data.table", "platetools", "htmltools", "DT", "logger", "bit64"), repos = "https://cran.rstudio.com")' && \
+  Rscript -e 'options(warn = 2); install.packages("oaStyle", repos = c(rdepot = "https://repos.openanalytics.eu/repo/public", getOption("repos")))'
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2025-03-25T15:33:58Z"
+LABEL org.opencontainers.image.created="2025-04-01T15:16:03Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="1561d769c65192a820053a565654dee8cbe55588"
+LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
@@ -593,6 +579,46 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "create_report save-params"
+  echo ""
+  echo "Create a basic QC report in HTML format based on a number of esets."
+  echo ""
+  echo "Arguments:"
+  echo "    --eset"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo ""
+  echo "    --output_report"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: report.html"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''