Build branch main with version main (5f6516e)

Build pipeline: viash-hub.biobox.main-v9whr

Source commit: 5f6516e9c0

Source message: Bump viash version (#172)

* bump viash version

* fix agat requirements

target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml

@@ -68,6 +68,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -174,16 +177,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/rseqc/rseqc_bamstat"
   executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:

target/executable/rseqc/rseqc_bamstat/rseqc_bamstat

@@ -2,7 +2,7 @@
 
 # rseqc_bamstat main
 # 
-# 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.
 # 
@@ -172,28 +172,6 @@ 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 "rseqc_bamstat main"
-  echo ""
-  echo "Generate statistics from a bam file."
-  echo ""
-  echo "Input:"
-  echo "    -i, --input_file"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input alignment file in BAM or SAM format."
-  echo ""
-  echo "    -q, --mapq"
-  echo "        type: integer"
-  echo "        example: 30"
-  echo "        Minimum mapping quality (phred scaled) to determine uniquely mapped"
-  echo "        reads. Default: '30'."
-  echo ""
-  echo "Output:"
-  echo "    --output"
-  echo "        type: file, output, file must exist"
-  echo "        Output file (txt) with mapping quality statistics."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -477,9 +455,9 @@ RUN echo "RSeQC bam_stat.py: $(bam_stat.py --version | cut -d' ' -f2-)" > /var/s
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:37Z"
 LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -594,6 +572,54 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "rseqc_bamstat main"
+  echo ""
+  echo "Generate statistics from a bam file."
+  echo ""
+  echo "Input:"
+  echo "    -i, --input_file"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input alignment file in BAM or SAM format."
+  echo ""
+  echo "    -q, --mapq"
+  echo "        type: integer"
+  echo "        example: 30"
+  echo "        Minimum mapping quality (phred scaled) to determine uniquely mapped"
+  echo "        reads. Default: '30'."
+  echo ""
+  echo "Output:"
+  echo "    --output"
+  echo "        type: file, output, file must exist"
+  echo "        Output file (txt) with mapping quality statistics."
+  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=''