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Build branch v0.3 with version v0.3.5 (18e092d)

Browse Source 
Build pipeline: viash-hub.demultiplex.v0.3-ldxlr

Source commit: 18e092d169

Source message: Bump version to 0.3.5
This commit is contained in:
CI
2025-03-04 13:36:18 +00:00
parent 4d7688483b
commit 78f3a8b65e
45 changed files with 601 additions and 225 deletions
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14
target/executable/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "interop_summary_to_csv"
namespace: "io"
version: "v0.3.4"
version: "v0.3.5"
argument_groups:
- name: "Input arguments"
arguments:
@@ -121,7 +121,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.4"
target_tag: "v0.3.5"
namespace_separator: "/"
setup:
- type: "apt"
@@ -146,12 +146,12 @@ build_info:
output: "target/executable/io/interop_summary_to_csv"
executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
viash_version: "0.9.0"
git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
git_tag: "v0.3.3-3-ge6f8b20"
git_commit: "18e092d169cc2704a2e4e705485d9231911d0484"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.4-6-g18e092d"
package_config:
name: "demultiplex"
version: "v0.3.4"
version: "v0.3.5"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -167,7 +167,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.5'"
keywords:
- "bioinformatics"
- "sequence"

14
target/executable/io/interop_summary_to_csv/interop_summary_to_csv
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# interop_summary_to_csv v0.3.4
# interop_summary_to_csv v0.3.5
#
# 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "interop_summary_to_csv v0.3.4"
echo "interop_summary_to_csv v0.3.5"
echo ""
echo "Input arguments:"
echo " --input"
@@ -470,10 +470,10 @@ 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="2024-12-20T12:37:34Z"
LABEL org.opencontainers.image.created="2025-03-04T13:21:45Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
LABEL org.opencontainers.image.version="v0.3.4"
LABEL org.opencontainers.image.revision="18e092d169cc2704a2e4e705485d9231911d0484"
LABEL org.opencontainers.image.version="v0.3.5"
VIASHDOCKER
fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "interop_summary_to_csv v0.3.4"
echo "interop_summary_to_csv v0.3.5"
exit
;;
--input)
@@ -733,7 +733,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.4'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.5'
fi
# print dockerfile

16
target/executable/io/publish/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "publish"
namespace: "io"
version: "v0.3.4"
version: "v0.3.5"
argument_groups:
- name: "Input arguments"
arguments:
@@ -22,7 +22,7 @@ argument_groups:
create_parent: true
required: true
direction: "input"
multiple: false
multiple: true
multiple_sep: ";"
- type: "file"
name: "--input_multiqc"
@@ -178,7 +178,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.4"
target_tag: "v0.3.5"
namespace_separator: "/"
setup:
- type: "apt"
@@ -196,12 +196,12 @@ build_info:
output: "target/executable/io/publish"
executable: "target/executable/io/publish/publish"
viash_version: "0.9.0"
git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
git_tag: "v0.3.3-3-ge6f8b20"
git_commit: "18e092d169cc2704a2e4e705485d9231911d0484"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.4-6-g18e092d"
package_config:
name: "demultiplex"
version: "v0.3.4"
version: "v0.3.5"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -217,7 +217,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.5'"
keywords:
- "bioinformatics"
- "sequence"

76
target/executable/io/publish/publish
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# publish v0.3.4
# publish v0.3.5
#
# 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "publish v0.3.4"
echo "publish v0.3.5"
echo ""
echo "Publish the processed results of the run"
echo ""
@@ -181,7 +181,7 @@ function ViashHelp {
echo " Directory to write fastq data to"
echo ""
echo " --input_falco"
echo " type: file, required parameter, file must exist"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " Directory to write falco output to"
echo ""
echo " --input_multiqc"
@@ -490,10 +490,10 @@ 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="2024-12-20T12:37:34Z"
LABEL org.opencontainers.image.created="2025-03-04T13:21:46Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
LABEL org.opencontainers.image.version="v0.3.4"
LABEL org.opencontainers.image.revision="18e092d169cc2704a2e4e705485d9231911d0484"
LABEL org.opencontainers.image.version="v0.3.5"
VIASHDOCKER
fi
@@ -629,7 +629,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "publish v0.3.4"
echo "publish v0.3.5"
exit
;;
--input)
@@ -644,14 +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 "$1")
fi
shift 1
;;
--input_multiqc)
@@ -808,7 +814,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.4'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.5'
fi
# print dockerfile
@@ -952,9 +958,17 @@ if [ ! -z "$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."
@@ -1070,8 +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")" )
@@ -1203,7 +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"
)
@@ -1224,6 +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 "\$!"
@@ -1238,7 +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")

14
target/executable/io/untar/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "untar"
namespace: "io"
version: "v0.3.4"
version: "v0.3.5"
argument_groups:
- name: "Input arguments"
arguments:
@@ -135,7 +135,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.4"
target_tag: "v0.3.5"
namespace_separator: "/"
setup:
- type: "apt"
@@ -153,12 +153,12 @@ build_info:
output: "target/executable/io/untar"
executable: "target/executable/io/untar/untar"
viash_version: "0.9.0"
git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
git_tag: "v0.3.3-3-ge6f8b20"
git_commit: "18e092d169cc2704a2e4e705485d9231911d0484"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.4-6-g18e092d"
package_config:
name: "demultiplex"
version: "v0.3.4"
version: "v0.3.5"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -174,7 +174,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.5'"
keywords:
- "bioinformatics"
- "sequence"

14
target/executable/io/untar/untar
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# untar v0.3.4
# untar v0.3.5
#
# 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "untar v0.3.4"
echo "untar v0.3.5"
echo ""
echo "Unpack a .tar file. When the contents of the .tar file is just a single"
echo "directory,"
@@ -476,10 +476,10 @@ 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="2024-12-20T12:37:34Z"
LABEL org.opencontainers.image.created="2025-03-04T13:21:46Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
LABEL org.opencontainers.image.version="v0.3.4"
LABEL org.opencontainers.image.revision="18e092d169cc2704a2e4e705485d9231911d0484"
LABEL org.opencontainers.image.version="v0.3.5"
VIASHDOCKER
fi
@@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "untar v0.3.4"
echo "untar v0.3.5"
exit
;;
--input)
@@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.4'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.5'
fi
# print dockerfile