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Build branch main with version main (f591b78)

Browse Source 
Build pipeline: viash-hub.demultiplex.main-p5t6v

Source commit: f591b7849f

Source message: Output demultiplexer log files (#41)
This commit is contained in:
CI
2025-05-14 08:38:23 +00:00
parent 9660348996
commit b720ad07f9
40 changed files with 759 additions and 105 deletions
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10
target/executable/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -41,6 +41,12 @@ resources:
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
- type: "file"
path: "iseq-DI"
info: null
status: "enabled"
scope:
@@ -151,9 +157,9 @@ build_info:
output: "target/executable/io/interop_summary_to_csv"
executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
viash_version: "0.9.4"
git_commit: "7a14841ac6d2aeac5a647dc896550e9474124bb3"
git_commit: "f591b7849fe63b27602b2a759c1089d5dee1ecaa"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-25-g7a14841"
git_tag: "v0.1.1-28-gf591b78"
package_config:
name: "demultiplex"
version: "main"

4
target/executable/io/interop_summary_to_csv/interop_summary_to_csv
View File

@@ -454,9 +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="2025-04-29T14:41:51Z"
LABEL org.opencontainers.image.created="2025-05-14T08:05:50Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="7a14841ac6d2aeac5a647dc896550e9474124bb3"
LABEL org.opencontainers.image.revision="f591b7849fe63b27602b2a759c1089d5dee1ecaa"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/io/publish/.config.vsh.yaml
View File

@@ -44,6 +44,15 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--input_demultiplexer_logs"
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output arguments"
arguments:
- type: "file"
@@ -90,6 +99,17 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--output_demultiplexer_logs"
info: null
default:
- "demultiplexer_logs"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "code.sh"
@@ -199,9 +219,9 @@ build_info:
output: "target/executable/io/publish"
executable: "target/executable/io/publish/publish"
viash_version: "0.9.4"
git_commit: "7a14841ac6d2aeac5a647dc896550e9474124bb3"
git_commit: "f591b7849fe63b27602b2a759c1089d5dee1ecaa"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-25-g7a14841"
git_tag: "v0.1.1-28-gf591b78"
package_config:
name: "demultiplex"
version: "main"

69
target/executable/io/publish/publish
View File

@@ -450,9 +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="2025-04-29T14:41:50Z"
LABEL org.opencontainers.image.created="2025-05-14T08:05:50Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="7a14841ac6d2aeac5a647dc896550e9474124bb3"
LABEL org.opencontainers.image.revision="f591b7849fe63b27602b2a759c1089d5dee1ecaa"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -591,6 +591,9 @@ function ViashHelp {
echo " type: file, required parameter, file must exist"
echo " Location where to write the run information to."
echo ""
echo " --input_demultiplexer_logs"
echo " type: file, required parameter, file must exist"
echo ""
echo "Output arguments:"
echo " --output"
echo " type: file, output, file must exist"
@@ -608,6 +611,10 @@ function ViashHelp {
echo " type: file, output, file must exist"
echo " default: run_information.csv"
echo ""
echo " --output_demultiplexer_logs"
echo " type: file, output, file must exist"
echo " default: demultiplexer_logs"
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
@@ -708,6 +715,17 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashRemoveFlags "$1")
shift 1
;;
--input_demultiplexer_logs)
[ -n "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--input_demultiplexer_logs\': \'$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --input_demultiplexer_logs. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--input_demultiplexer_logs=*)
[ -n "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--input_demultiplexer_logs=*\': \'$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(ViashRemoveFlags "$1")
shift 1
;;
--output)
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPUT="$2"
@@ -752,6 +770,17 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashRemoveFlags "$1")
shift 1
;;
--output_demultiplexer_logs)
[ -n "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--output_demultiplexer_logs\': \'$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output_demultiplexer_logs. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--output_demultiplexer_logs=*)
[ -n "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--output_demultiplexer_logs=*\': \'$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
VIASH_ENGINE_ID="$2"
shift 2
@@ -940,6 +969,10 @@ if [ -z ${VIASH_PAR_INPUT_RUN_INFORMATION+x} ]; then
ViashError '--input_run_information' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS+x} ]; then
ViashError '--input_demultiplexer_logs' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
exit 1
@@ -978,6 +1011,9 @@ fi
if [ -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then
VIASH_PAR_OUTPUT_RUN_INFORMATION="run_information.csv"
fi
if [ -z ${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS+x} ]; then
VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS="demultiplexer_logs"
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
@@ -1004,6 +1040,10 @@ if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ] && [ ! -e "$VIASH_PAR_INPUT_RUN_I
ViashError "Input file '$VIASH_PAR_INPUT_RUN_INFORMATION' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && [ ! -e "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then
ViashError "Input file '$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS' does not exist."
exit 1
fi
# check whether parameters values are of the right type
if [[ -n "$VIASH_META_CPUS" ]]; then
@@ -1092,6 +1132,9 @@ fi
if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_RUN_INFORMATION")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_RUN_INFORMATION")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")"
fi
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
if [ "$VIASH_MODE" == "run" ]; then
@@ -1128,6 +1171,10 @@ if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_RUN_INFORMATION")" )
VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_RUN_INFORMATION")
fi
if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS")" )
VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
@@ -1148,6 +1195,11 @@ if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ]; then
VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_RUN_INFORMATION")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_RUN_INFORMATION" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")" )
VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
@@ -1221,10 +1273,12 @@ $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'
$( if [ ! -z ${VIASH_PAR_INPUT_FALCO+x} ]; then echo "${VIASH_PAR_INPUT_FALCO}" | sed "s#'#'\"'\"'#g;s#.*#par_input_falco='&'#" ; else echo "# par_input_falco="; fi )
$( if [ ! -z ${VIASH_PAR_INPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_INPUT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_input_multiqc='&'#" ; else echo "# par_input_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_INPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_INPUT_RUN_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_input_run_information='&'#" ; else echo "# par_input_run_information="; fi )
$( if [ ! -z ${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_input_demultiplexer_logs='&'#" ; else echo "# par_input_demultiplexer_logs="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_FALCO+x} ]; then echo "${VIASH_PAR_OUTPUT_FALCO}" | sed "s#'#'\"'\"'#g;s#.*#par_output_falco='&'#" ; else echo "# par_output_falco="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_OUTPUT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_output_multiqc='&'#" ; else echo "# par_output_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_OUTPUT_RUN_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_output_run_information='&'#" ; else echo "# par_output_run_information="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_output_demultiplexer_logs='&'#" ; else echo "# par_output_demultiplexer_logs="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
@@ -1252,6 +1306,7 @@ set -eo pipefail
declare -A input_output_mapping=(["par_input"]="par_output"
["par_input_multiqc"]="par_output_multiqc"
["par_input_run_information"]="par_output_run_information"
["par_input_demultiplexer_logs"]="par_output_demultiplexer_logs"
)
for input_argument_name in "\${!input_output_mapping[@]}"
@@ -1310,6 +1365,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ]; then
VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_RUN_INFORMATION")
fi
if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then
VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
fi
@@ -1322,6 +1380,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ]; then
VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_RUN_INFORMATION")
fi
if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then
VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
fi
@@ -1354,6 +1415,10 @@ if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ] && [ ! -e "$VIASH_PAR_OUTPUT_RUN
ViashError "Output file '$VIASH_PAR_OUTPUT_RUN_INFORMATION' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && [ ! -e "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then
ViashError "Output file '$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS' does not exist."
exit 1
fi
exit 0

4
target/executable/io/untar/.config.vsh.yaml
View File

@@ -156,9 +156,9 @@ build_info:
output: "target/executable/io/untar"
executable: "target/executable/io/untar/untar"
viash_version: "0.9.4"
git_commit: "7a14841ac6d2aeac5a647dc896550e9474124bb3"
git_commit: "f591b7849fe63b27602b2a759c1089d5dee1ecaa"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-25-g7a14841"
git_tag: "v0.1.1-28-gf591b78"
package_config:
name: "demultiplex"
version: "main"

4
target/executable/io/untar/untar
View File

@@ -450,9 +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="2025-04-29T14:41:50Z"
LABEL org.opencontainers.image.created="2025-05-14T08:05:49Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="7a14841ac6d2aeac5a647dc896550e9474124bb3"
LABEL org.opencontainers.image.revision="f591b7849fe63b27602b2a759c1089d5dee1ecaa"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER