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Build branch main with version main (795abd6)

Browse Source 
Build pipeline: viash-hub.demultiplex.main-4xxbp

Source commit: 795abd6868

Source message: Run Falco in parallel for each well (#33)
This commit is contained in:
CI
2025-03-04 06:00:00 +00:00
parent eb8d600efc
commit e16f7d7290
35 changed files with 988 additions and 2491 deletions
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13
target/executable/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -43,9 +43,6 @@ resources:
dest: "nextflow_labels.config"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -148,10 +145,10 @@ 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: "0.9.1"
git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-16-gdd1f934"
viash_version: "0.9.0"
git_commit: "795abd68688f4f31b0587bc8e4a7de49b6c00825"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g795abd6"
package_config:
name: "demultiplex"
version: "main"
@@ -160,7 +157,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/demultiplex/v2/"
dest: "testData"
viash_version: "0.9.1"
viash_version: "0.9.0"
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 0.9.1 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -169,6 +169,22 @@ 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'
@@ -454,9 +470,9 @@ 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="2025-01-14T11:56:35Z"
LABEL org.opencontainers.image.created="2025-03-04T05:45:47Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="dd1f93487f4e908999504e1fcdf97f6c59f743d9"
LABEL org.opencontainers.image.revision="795abd68688f4f31b0587bc8e4a7de49b6c00825"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -571,48 +587,6 @@ 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=''

15
target/executable/io/publish/.config.vsh.yaml
View File

@@ -22,7 +22,7 @@ argument_groups:
create_parent: true
required: true
direction: "input"
multiple: false
multiple: true
multiple_sep: ";"
- type: "file"
name: "--input_multiqc"
@@ -100,9 +100,6 @@ resources:
description: "Publish the processed results of the run"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -198,10 +195,10 @@ build_info:
engine: "docker|native"
output: "target/executable/io/publish"
executable: "target/executable/io/publish/publish"
viash_version: "0.9.1"
git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-16-gdd1f934"
viash_version: "0.9.0"
git_commit: "795abd68688f4f31b0587bc8e4a7de49b6c00825"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g795abd6"
package_config:
name: "demultiplex"
version: "main"
@@ -210,7 +207,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/demultiplex/v2/"
dest: "testData"
viash_version: "0.9.1"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

172
target/executable/io/publish/publish
View File

@@ -2,7 +2,7 @@
# publish main
#
# This wrapper script is auto-generated by viash 0.9.1 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -169,6 +169,46 @@ 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'
@@ -450,9 +490,9 @@ 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="2025-01-14T11:56:35Z"
LABEL org.opencontainers.image.created="2025-03-04T05:45:47Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="dd1f93487f4e908999504e1fcdf97f6c59f743d9"
LABEL org.opencontainers.image.revision="795abd68688f4f31b0587bc8e4a7de49b6c00825"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -567,72 +607,6 @@ 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, 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=''
@@ -670,14 +644,20 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--input_falco)
[ -n "$VIASH_PAR_INPUT_FALCO" ] && ViashError Bad arguments for option \'--input_falco\': \'$VIASH_PAR_INPUT_FALCO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_INPUT_FALCO="$2"
if [ -z "$VIASH_PAR_INPUT_FALCO" ]; then
VIASH_PAR_INPUT_FALCO="$2"
else
VIASH_PAR_INPUT_FALCO="$VIASH_PAR_INPUT_FALCO;""$2"
fi
[ $# -lt 2 ] && ViashError Not enough arguments passed to --input_falco. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--input_falco=*)
[ -n "$VIASH_PAR_INPUT_FALCO" ] && ViashError Bad arguments for option \'--input_falco=*\': \'$VIASH_PAR_INPUT_FALCO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_INPUT_FALCO=$(ViashRemoveFlags "$1")
if [ -z "$VIASH_PAR_INPUT_FALCO" ]; then
VIASH_PAR_INPUT_FALCO=$(ViashRemoveFlags "$1")
else
VIASH_PAR_INPUT_FALCO="$VIASH_PAR_INPUT_FALCO;"$(ViashRemoveFlags "$1")
fi
shift 1
;;
--input_multiqc)
@@ -978,9 +958,17 @@ if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
ViashError "Input file '$VIASH_PAR_INPUT' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_INPUT_FALCO" ] && [ ! -e "$VIASH_PAR_INPUT_FALCO" ]; then
ViashError "Input file '$VIASH_PAR_INPUT_FALCO' does not exist."
exit 1
if [ ! -z "$VIASH_PAR_INPUT_FALCO" ]; then
IFS=';'
set -f
for file in $VIASH_PAR_INPUT_FALCO; do
unset IFS
if [ ! -e "$file" ]; then
ViashError "Input file '$file' does not exist."
exit 1
fi
done
set +f
fi
if [ ! -z "$VIASH_PAR_INPUT_MULTIQC" ] && [ ! -e "$VIASH_PAR_INPUT_MULTIQC" ]; then
ViashError "Input file '$VIASH_PAR_INPUT_MULTIQC' does not exist."
@@ -1096,8 +1084,15 @@ if [ ! -z "$VIASH_PAR_INPUT" ]; then
VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT")
fi
if [ ! -z "$VIASH_PAR_INPUT_FALCO" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_FALCO")" )
VIASH_PAR_INPUT_FALCO=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_FALCO")
VIASH_TEST_INPUT_FALCO=()
IFS=';'
for var in $VIASH_PAR_INPUT_FALCO; do
unset IFS
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
var=$(ViashDockerAutodetectMount "$var")
VIASH_TEST_INPUT_FALCO+=( "$var" )
done
VIASH_PAR_INPUT_FALCO=$(IFS=';' ; echo "${VIASH_TEST_INPUT_FALCO[*]}")
fi
if [ ! -z "$VIASH_PAR_INPUT_MULTIQC" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_MULTIQC")" )
@@ -1229,7 +1224,6 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
set -eo pipefail
declare -A input_output_mapping=(["par_input"]="par_output"
["par_input_falco"]="par_output_falco"
["par_input_multiqc"]="par_output_multiqc"
["par_input_run_information"]="par_output_run_information"
)
@@ -1250,6 +1244,14 @@ do
echo "Output files for \$output_location:"
ls "\$output_location"
done
echo "Grouping output from \$par_input_falco into \$par_output_falco"
mkdir -p "\$par_output_falco"
IFS=";" read -ra falco_inputs <<< \$par_input_falco
for falco_dir in "\${falco_inputs[@]}"; do
echo "Copying contents of \$falco_dir"
find -H -D exec "\$falco_dir" -type f -maxdepth 1 -exec cp -t "\$par_output_falco" {} +
done
VIASHMAIN
bash "\$tempscript" &
wait "\$!"
@@ -1264,7 +1266,17 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
VIASH_PAR_INPUT=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT")
fi
if [ ! -z "$VIASH_PAR_INPUT_FALCO" ]; then
VIASH_PAR_INPUT_FALCO=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_FALCO")
unset VIASH_TEST_INPUT_FALCO
IFS=';'
for var in $VIASH_PAR_INPUT_FALCO; do
unset IFS
if [ -z "$VIASH_TEST_INPUT_FALCO" ]; then
VIASH_TEST_INPUT_FALCO="$(ViashDockerStripAutomount "$var")"
else
VIASH_TEST_INPUT_FALCO="$VIASH_TEST_INPUT_FALCO;""$(ViashDockerStripAutomount "$var")"
fi
done
VIASH_PAR_INPUT_FALCO="$VIASH_TEST_INPUT_FALCO"
fi
if [ ! -z "$VIASH_PAR_INPUT_MULTIQC" ]; then
VIASH_PAR_INPUT_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_MULTIQC")

13
target/executable/io/untar/.config.vsh.yaml
View File

@@ -57,9 +57,6 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -155,10 +152,10 @@ build_info:
engine: "docker|native"
output: "target/executable/io/untar"
executable: "target/executable/io/untar/untar"
viash_version: "0.9.1"
git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9"
git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-16-gdd1f934"
viash_version: "0.9.0"
git_commit: "795abd68688f4f31b0587bc8e4a7de49b6c00825"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g795abd6"
package_config:
name: "demultiplex"
version: "main"
@@ -167,7 +164,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/demultiplex/v2/"
dest: "testData"
viash_version: "0.9.1"
viash_version: "0.9.0"
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 0.9.1 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -169,6 +169,32 @@ 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'
@@ -450,9 +476,9 @@ 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="2025-01-14T11:56:35Z"
LABEL org.opencontainers.image.created="2025-03-04T05:45:47Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="dd1f93487f4e908999504e1fcdf97f6c59f743d9"
LABEL org.opencontainers.image.revision="795abd68688f4f31b0587bc8e4a7de49b6c00825"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -567,58 +593,6 @@ 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=''