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Build branch main with version main (162497a)

Browse Source 
Build pipeline: viash-hub.demultiplex.main-ss9kt

Source commit: 162497ab73

Source message: Bump viash to 0.9.3 (#43)

* Bump viash to 0.9.3

* Add CHANGELOG
This commit is contained in:
CI
2025-04-22 12:11:00 +00:00
parent 51fdf9e8bf
commit eb6fd9e999
22 changed files with 2468 additions and 646 deletions
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11
target/executable/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -43,6 +43,9 @@ resources:
dest: "nextflow_labels.config"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -145,10 +148,10 @@ build_info:
engine: "docker|native"
output: "target/executable/io/interop_summary_to_csv"
executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
viash_version: "0.9.0"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
viash_version: "0.9.3"
git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-g0c27ec1"
git_tag: "v0.1.1-22-g162497a"
package_config:
name: "demultiplex"
version: "main"
@@ -157,7 +160,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/demultiplex/v2/"
dest: "testData"
viash_version: "0.9.0"
viash_version: "0.9.3"
source: "src"
target: "target"
config_mods:

64
target/executable/io/interop_summary_to_csv/interop_summary_to_csv
View File

@@ -2,7 +2,7 @@
# interop_summary_to_csv 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 0.9.3 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -169,22 +169,6 @@ 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 "interop_summary_to_csv main"
echo ""
echo "Input arguments:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " Sequencing run folder (*not* InterOp folder)."
echo ""
echo "Output arguments:"
echo " --output_run_summary"
echo " type: file, required parameter, output, file must exist"
echo ""
echo " --output_index_summary"
echo " type: file, required parameter, output, file must exist"
}
# initialise variables
VIASH_MODE='run'
@@ -470,9 +454,9 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
LABEL org.opencontainers.image.created="2025-03-27T15:56:06Z"
LABEL org.opencontainers.image.created="2025-04-22T11:54:46Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
LABEL org.opencontainers.image.revision="162497ab73faf321d5166fe34cd1f6976b14dcb0"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -587,6 +571,48 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "interop_summary_to_csv main"
echo ""
echo "Input arguments:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " Sequencing run folder (*not* InterOp folder)."
echo ""
echo "Output arguments:"
echo " --output_run_summary"
echo " type: file, required parameter, output, file must exist"
echo ""
echo " --output_index_summary"
echo " type: file, required parameter, output, file must exist"
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=''

11
target/executable/io/publish/.config.vsh.yaml
View File

@@ -100,6 +100,9 @@ resources:
description: "Publish the processed results of the run"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -195,10 +198,10 @@ build_info:
engine: "docker|native"
output: "target/executable/io/publish"
executable: "target/executable/io/publish/publish"
viash_version: "0.9.0"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
viash_version: "0.9.3"
git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-g0c27ec1"
git_tag: "v0.1.1-22-g162497a"
package_config:
name: "demultiplex"
version: "main"
@@ -207,7 +210,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/demultiplex/v2/"
dest: "testData"
viash_version: "0.9.0"
viash_version: "0.9.3"
source: "src"
target: "target"
config_mods:

112
target/executable/io/publish/publish
View File

@@ -2,7 +2,7 @@
# publish 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 0.9.3 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -169,46 +169,6 @@ 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 "publish main"
echo ""
echo "Publish the processed results of the run"
echo ""
echo "Input arguments:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " Directory to write fastq data to"
echo ""
echo " --input_falco"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " Directory to write falco output to"
echo ""
echo " --input_multiqc"
echo " type: file, required parameter, file must exist"
echo " Location where to write the MultiQC report to."
echo ""
echo " --input_run_information"
echo " type: file, required parameter, file must exist"
echo " Location where to write the run information to."
echo ""
echo "Output arguments:"
echo " --output"
echo " type: file, output, file must exist"
echo " default: fastq"
echo ""
echo " --output_falco"
echo " type: file, output, file must exist"
echo " default: qc/fastqc"
echo ""
echo " --output_multiqc"
echo " type: file, output, file must exist"
echo " default: qc/multiqc_report.html"
echo ""
echo " --output_run_information"
echo " type: file, output, file must exist"
echo " default: run_information.csv"
}
# initialise variables
VIASH_MODE='run'
@@ -490,9 +450,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish"
LABEL org.opencontainers.image.created="2025-03-27T15:56:05Z"
LABEL org.opencontainers.image.created="2025-04-22T11:54:46Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
LABEL org.opencontainers.image.revision="162497ab73faf321d5166fe34cd1f6976b14dcb0"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -607,6 +567,72 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "publish main"
echo ""
echo "Publish the processed results of the run"
echo ""
echo "Input arguments:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " Directory to write fastq data to"
echo ""
echo " --input_falco"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " Directory to write falco output to"
echo ""
echo " --input_multiqc"
echo " type: file, required parameter, file must exist"
echo " Location where to write the MultiQC report to."
echo ""
echo " --input_run_information"
echo " type: file, required parameter, file must exist"
echo " Location where to write the run information to."
echo ""
echo "Output arguments:"
echo " --output"
echo " type: file, output, file must exist"
echo " default: fastq"
echo ""
echo " --output_falco"
echo " type: file, output, file must exist"
echo " default: qc/fastqc"
echo ""
echo " --output_multiqc"
echo " type: file, output, file must exist"
echo " default: qc/multiqc_report.html"
echo ""
echo " --output_run_information"
echo " type: file, output, file must exist"
echo " default: run_information.csv"
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=''

11
target/executable/io/untar/.config.vsh.yaml
View File

@@ -57,6 +57,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -152,10 +155,10 @@ build_info:
engine: "docker|native"
output: "target/executable/io/untar"
executable: "target/executable/io/untar/untar"
viash_version: "0.9.0"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
viash_version: "0.9.3"
git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-g0c27ec1"
git_tag: "v0.1.1-22-g162497a"
package_config:
name: "demultiplex"
version: "main"
@@ -164,7 +167,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/demultiplex/v2/"
dest: "testData"
viash_version: "0.9.0"
viash_version: "0.9.3"
source: "src"
target: "target"
config_mods:

84
target/executable/io/untar/untar
View File

@@ -2,7 +2,7 @@
# untar 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 0.9.3 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -169,32 +169,6 @@ 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 "untar main"
echo ""
echo "Unpack a .tar file. When the contents of the .tar file is just a single"
echo "directory,"
echo "put the contents of the directory into the output folder instead of that"
echo "directory."
echo ""
echo "Input arguments:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " Tarball file to be unpacked."
echo ""
echo "Output arguments:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " Directory to write the contents of the .tar file to."
echo ""
echo "Other arguments:"
echo " -e, --exclude"
echo " type: string"
echo " example: docs/figures"
echo " Prevents any file or member whose name matches the shell wildcard"
echo " (pattern) from being extracted."
}
# initialise variables
VIASH_MODE='run'
@@ -476,9 +450,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io untar"
LABEL org.opencontainers.image.created="2025-03-27T15:56:05Z"
LABEL org.opencontainers.image.created="2025-04-22T11:54:46Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
LABEL org.opencontainers.image.revision="162497ab73faf321d5166fe34cd1f6976b14dcb0"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -593,6 +567,58 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "untar main"
echo ""
echo "Unpack a .tar file. When the contents of the .tar file is just a single"
echo "directory,"
echo "put the contents of the directory into the output folder instead of that"
echo "directory."
echo ""
echo "Input arguments:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " Tarball file to be unpacked."
echo ""
echo "Output arguments:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " Directory to write the contents of the .tar file to."
echo ""
echo "Other arguments:"
echo " -e, --exclude"
echo " type: string"
echo " example: docs/figures"
echo " Prevents any file or member whose name matches the shell wildcard"
echo " (pattern) from being extracted."
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=''