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Build branch outflow with version outflow (a63bf11)

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Build pipeline: viash-hub.demultiplex.outflow-n2g7r

Source commit: a63bf1179f

Source message: Update container for publish component
This commit is contained in:
CI
2024-12-11 07:38:36 +00:00
parent 906e5c4a4b
commit 4ec9fa3389
23 changed files with 132 additions and 122 deletions
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21
src/io/publish/code.sh
View File

@@ -1,17 +1,20 @@
#!/bin/bash
# Create output directory
mkdir -p "$par_output"
mkdir -p "$par_output_falco"
echo "Publishing $par_input -> $par_output"
echo "Publishing $par_input_falco -> $par_output_falco"
echo "Publishing $par_input_multiqc -> $par_output_multiqc"
echo
echo "par_output: $par_output"
echo "par_output_falco: $par_output_falco"
echo "par_output_multiqc: $par_output_multiqc"
echo "Creating directory if it does not exist:"
mkdir -p $(dirname "$par_output") && echo "Containing directory $par_output created"
mkdir -p $(dirname "$par_output_falco") && echo "Containing directory $par_output_falco created"
mkdir -p $(dirname "$par_output_multiqc") && echo "Containing directory $par_output_multiqc created"
cp -L "$par_input"/* "$par_output"
cp -rL "$par_input_falco"/* "$par_output_falco"
cp -L "$par_input_multiqc" "$par_output_multiqc"
echo
echo "Copying files..."
cp -rL "$par_input" "$par_output"
cp -rL "$par_input_falco" "$par_output_falco"
cp -rL "$par_input_multiqc" "$par_output_multiqc"
echo
echo "Output files:"

7
src/io/publish/config.vsh.yaml
View File

@@ -37,10 +37,11 @@ resources:
engines:
- type: docker
image: debian:stable-20220912
image: debian:stable-slim
setup:
- type: docker
run: apt update && apt install -y procps
- type: apt
packages:
- procps
runners:
- type: executable

17
src/runner/main.nf
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@@ -1,7 +1,7 @@
def date = new Date().format('yyyyMMdd_hhmmss')
def viash_config = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() + "/_viash.yaml"
def version = get_version(file(viash_config).text)
def version = get_version(viash_config)
workflow run_wf {
take:
@@ -58,13 +58,10 @@ workflow run_wf {
output_ch
}
def get_version(txt) {
matcher = txt =~ /(?m)^version:\s+(.*)$/
if (matcher.size() == 0) {
println("No version found, setting version to 'unknown_version'")
return "unknown_version"
} else {
println("Version found: ${matcher[0][1]}")
return matcher[0][1]
}
def get_version(inputFile) {
def yamlSlurper = new groovy.yaml.YamlSlurper()
def loaded_viash_config = yamlSlurper.parse(file(inputFile))
def version = (loaded_viash_config.version) ? loaded_viash_config.version : "unknown_version"
println("Version to be used: ${version}")
return version
}

6
target/executable/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -141,9 +141,9 @@ build_info:
output: "target/executable/io/interop_summary_to_csv"
executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
viash_version: "0.9.0"
git_commit: "3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
git_remote: "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g3e2efbe"
git_commit: "a63bf1179fff7e98e7210310cef76ca8b16de00b"
git_remote: "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-ga63bf11"
package_config:
name: "demultiplex"
version: "outflow"

4
target/executable/io/interop_summary_to_csv/interop_summary_to_csv
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@@ -470,9 +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="2024-12-10T15:10:43Z"
LABEL org.opencontainers.image.created="2024-12-11T07:23:19Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
LABEL org.opencontainers.image.revision="a63bf1179fff7e98e7210310cef76ca8b16de00b"
LABEL org.opencontainers.image.version="outflow"
VIASHDOCKER

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

@@ -150,14 +150,15 @@ runners:
engines:
- type: "docker"
id: "docker"
image: "debian:stable-20220912"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "outflow"
namespace_separator: "/"
setup:
- type: "docker"
run:
- "apt update && apt install -y procps"
- type: "apt"
packages:
- "procps"
interactive: false
entrypoint: []
cmd: null
- type: "native"
@@ -169,9 +170,9 @@ build_info:
output: "target/executable/io/publish"
executable: "target/executable/io/publish/publish"
viash_version: "0.9.0"
git_commit: "3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
git_remote: "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g3e2efbe"
git_commit: "a63bf1179fff7e98e7210310cef76ca8b16de00b"
git_remote: "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-ga63bf11"
package_config:
name: "demultiplex"
version: "outflow"

32
target/executable/io/publish/publish
View File

@@ -475,13 +475,16 @@ function ViashDockerfile {
if [[ "$engine_id" == "docker" ]]; then
cat << 'VIASHDOCKER'
FROM debian:stable-20220912
FROM debian:stable-slim
ENTRYPOINT []
RUN apt update && apt install -y procps
RUN apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y procps && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish"
LABEL org.opencontainers.image.created="2024-12-10T15:10:44Z"
LABEL org.opencontainers.image.created="2024-12-11T07:23:19Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
LABEL org.opencontainers.image.revision="a63bf1179fff7e98e7210310cef76ca8b16de00b"
LABEL org.opencontainers.image.version="outflow"
VIASHDOCKER
@@ -1142,18 +1145,21 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
## VIASH END
#!/bin/bash
# Create output directory
mkdir -p "\$par_output"
mkdir -p "\$par_output_falco"
echo "Publishing \$par_input -> \$par_output"
echo "Publishing \$par_input_falco -> \$par_output_falco"
echo "Publishing \$par_input_multiqc -> \$par_output_multiqc"
echo
echo "par_output: \$par_output"
echo "par_output_falco: \$par_output_falco"
echo "par_output_multiqc: \$par_output_multiqc"
echo "Creating directory if it does not exist:"
mkdir -p \$(dirname "\$par_output") && echo "Containing directory \$par_output created"
mkdir -p \$(dirname "\$par_output_falco") && echo "Containing directory \$par_output_falco created"
mkdir -p \$(dirname "\$par_output_multiqc") && echo "Containing directory \$par_output_multiqc created"
cp -L "\$par_input"/* "\$par_output"
cp -rL "\$par_input_falco"/* "\$par_output_falco"
cp -L "\$par_input_multiqc" "\$par_output_multiqc"
echo
echo "Copying files..."
cp -rL "\$par_input" "\$par_output"
cp -rL "\$par_input_falco" "\$par_output_falco"
cp -rL "\$par_input_multiqc" "\$par_output_multiqc"
echo
echo "Output files:"

6
target/executable/io/untar/.config.vsh.yaml
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@@ -148,9 +148,9 @@ build_info:
output: "target/executable/io/untar"
executable: "target/executable/io/untar/untar"
viash_version: "0.9.0"
git_commit: "3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
git_remote: "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g3e2efbe"
git_commit: "a63bf1179fff7e98e7210310cef76ca8b16de00b"
git_remote: "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-ga63bf11"
package_config:
name: "demultiplex"
version: "outflow"

4
target/executable/io/untar/untar
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@@ -476,9 +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="2024-12-10T15:10:44Z"
LABEL org.opencontainers.image.created="2024-12-11T07:23:20Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
LABEL org.opencontainers.image.revision="a63bf1179fff7e98e7210310cef76ca8b16de00b"
LABEL org.opencontainers.image.version="outflow"
VIASHDOCKER

6
target/nextflow/dataflow/combine_samples/.config.vsh.yaml
View File

@@ -139,9 +139,9 @@ build_info:
output: "target/nextflow/dataflow/combine_samples"
executable: "target/nextflow/dataflow/combine_samples/main.nf"
viash_version: "0.9.0"
git_commit: "3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
git_remote: "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g3e2efbe"
git_commit: "a63bf1179fff7e98e7210310cef76ca8b16de00b"
git_remote: "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-ga63bf11"
package_config:
name: "demultiplex"
version: "outflow"

6
target/nextflow/dataflow/combine_samples/main.nf
View File

@@ -2972,9 +2972,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/combine_samples",
"viash_version" : "0.9.0",
"git_commit" : "3e2efbee8c2deafb1b68eab44c5b9640536c3cca",
"git_remote" : "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-18-g3e2efbe"
"git_commit" : "a63bf1179fff7e98e7210310cef76ca8b16de00b",
"git_remote" : "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-21-ga63bf11"
},
"package_config" : {
"name" : "demultiplex",

6
target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
View File

@@ -133,9 +133,9 @@ build_info:
output: "target/nextflow/dataflow/gather_fastqs_and_validate"
executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
viash_version: "0.9.0"
git_commit: "3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
git_remote: "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g3e2efbe"
git_commit: "a63bf1179fff7e98e7210310cef76ca8b16de00b"
git_remote: "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-ga63bf11"
package_config:
name: "demultiplex"
version: "outflow"

6
target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
View File

@@ -2965,9 +2965,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
"viash_version" : "0.9.0",
"git_commit" : "3e2efbee8c2deafb1b68eab44c5b9640536c3cca",
"git_remote" : "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-18-g3e2efbe"
"git_commit" : "a63bf1179fff7e98e7210310cef76ca8b16de00b",
"git_remote" : "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-21-ga63bf11"
},
"package_config" : {
"name" : "demultiplex",

6
target/nextflow/demultiplex/.config.vsh.yaml
View File

@@ -220,9 +220,9 @@ build_info:
output: "target/nextflow/demultiplex"
executable: "target/nextflow/demultiplex/main.nf"
viash_version: "0.9.0"
git_commit: "3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
git_remote: "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g3e2efbe"
git_commit: "a63bf1179fff7e98e7210310cef76ca8b16de00b"
git_remote: "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-ga63bf11"
dependencies:
- "target/nextflow/io/untar"
- "target/nextflow/dataflow/gather_fastqs_and_validate"

6
target/nextflow/demultiplex/main.nf
View File

@@ -3088,9 +3088,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/demultiplex",
"viash_version" : "0.9.0",
"git_commit" : "3e2efbee8c2deafb1b68eab44c5b9640536c3cca",
"git_remote" : "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-18-g3e2efbe"
"git_commit" : "a63bf1179fff7e98e7210310cef76ca8b16de00b",
"git_remote" : "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-21-ga63bf11"
},
"package_config" : {
"name" : "demultiplex",

6
target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -141,9 +141,9 @@ build_info:
output: "target/nextflow/io/interop_summary_to_csv"
executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
viash_version: "0.9.0"
git_commit: "3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
git_remote: "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g3e2efbe"
git_commit: "a63bf1179fff7e98e7210310cef76ca8b16de00b"
git_remote: "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-ga63bf11"
package_config:
name: "demultiplex"
version: "outflow"

6
target/nextflow/io/interop_summary_to_csv/main.nf
View File

@@ -2977,9 +2977,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/interop_summary_to_csv",
"viash_version" : "0.9.0",
"git_commit" : "3e2efbee8c2deafb1b68eab44c5b9640536c3cca",
"git_remote" : "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-18-g3e2efbe"
"git_commit" : "a63bf1179fff7e98e7210310cef76ca8b16de00b",
"git_remote" : "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-21-ga63bf11"
},
"package_config" : {
"name" : "demultiplex",

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

@@ -150,14 +150,15 @@ runners:
engines:
- type: "docker"
id: "docker"
image: "debian:stable-20220912"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "outflow"
namespace_separator: "/"
setup:
- type: "docker"
run:
- "apt update && apt install -y procps"
- type: "apt"
packages:
- "procps"
interactive: false
entrypoint: []
cmd: null
- type: "native"
@@ -169,9 +170,9 @@ build_info:
output: "target/nextflow/io/publish"
executable: "target/nextflow/io/publish/main.nf"
viash_version: "0.9.0"
git_commit: "3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
git_remote: "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g3e2efbe"
git_commit: "a63bf1179fff7e98e7210310cef76ca8b16de00b"
git_remote: "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-ga63bf11"
package_config:
name: "demultiplex"
version: "outflow"

38
target/nextflow/io/publish/main.nf
View File

@@ -2987,16 +2987,17 @@ meta = [
{
"type" : "docker",
"id" : "docker",
"image" : "debian:stable-20220912",
"image" : "debian:stable-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "outflow",
"namespace_separator" : "/",
"setup" : [
{
"type" : "docker",
"run" : [
"apt update && apt install -y procps"
]
"type" : "apt",
"packages" : [
"procps"
],
"interactive" : false
}
]
},
@@ -3011,9 +3012,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish",
"viash_version" : "0.9.0",
"git_commit" : "3e2efbee8c2deafb1b68eab44c5b9640536c3cca",
"git_remote" : "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-18-g3e2efbe"
"git_commit" : "a63bf1179fff7e98e7210310cef76ca8b16de00b",
"git_remote" : "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-21-ga63bf11"
},
"package_config" : {
"name" : "demultiplex",
@@ -3091,18 +3092,21 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
## VIASH END
#!/bin/bash
# Create output directory
mkdir -p "\\$par_output"
mkdir -p "\\$par_output_falco"
echo "Publishing \\$par_input -> \\$par_output"
echo "Publishing \\$par_input_falco -> \\$par_output_falco"
echo "Publishing \\$par_input_multiqc -> \\$par_output_multiqc"
echo
echo "par_output: \\$par_output"
echo "par_output_falco: \\$par_output_falco"
echo "par_output_multiqc: \\$par_output_multiqc"
echo "Creating directory if it does not exist:"
mkdir -p \\$(dirname "\\$par_output") && echo "Containing directory \\$par_output created"
mkdir -p \\$(dirname "\\$par_output_falco") && echo "Containing directory \\$par_output_falco created"
mkdir -p \\$(dirname "\\$par_output_multiqc") && echo "Containing directory \\$par_output_multiqc created"
cp -L "\\$par_input"/* "\\$par_output"
cp -rL "\\$par_input_falco"/* "\\$par_output_falco"
cp -L "\\$par_input_multiqc" "\\$par_output_multiqc"
echo
echo "Copying files..."
cp -rL "\\$par_input" "\\$par_output"
cp -rL "\\$par_input_falco" "\\$par_output_falco"
cp -rL "\\$par_input_multiqc" "\\$par_output_multiqc"
echo
echo "Output files:"

6
target/nextflow/io/untar/.config.vsh.yaml
View File

@@ -148,9 +148,9 @@ build_info:
output: "target/nextflow/io/untar"
executable: "target/nextflow/io/untar/main.nf"
viash_version: "0.9.0"
git_commit: "3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
git_remote: "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g3e2efbe"
git_commit: "a63bf1179fff7e98e7210310cef76ca8b16de00b"
git_remote: "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-ga63bf11"
package_config:
name: "demultiplex"
version: "outflow"

6
target/nextflow/io/untar/main.nf
View File

@@ -2989,9 +2989,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/untar",
"viash_version" : "0.9.0",
"git_commit" : "3e2efbee8c2deafb1b68eab44c5b9640536c3cca",
"git_remote" : "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-18-g3e2efbe"
"git_commit" : "a63bf1179fff7e98e7210310cef76ca8b16de00b",
"git_remote" : "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-21-ga63bf11"
},
"package_config" : {
"name" : "demultiplex",

6
target/nextflow/runner/.config.vsh.yaml
View File

@@ -156,9 +156,9 @@ build_info:
output: "target/nextflow/runner"
executable: "target/nextflow/runner/main.nf"
viash_version: "0.9.0"
git_commit: "3e2efbee8c2deafb1b68eab44c5b9640536c3cca"
git_remote: "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-18-g3e2efbe"
git_commit: "a63bf1179fff7e98e7210310cef76ca8b16de00b"
git_remote: "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-21-ga63bf11"
dependencies:
- "target/nextflow/demultiplex"
- "target/nextflow/io/publish"

23
target/nextflow/runner/main.nf
View File

@@ -3003,9 +3003,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/runner",
"viash_version" : "0.9.0",
"git_commit" : "3e2efbee8c2deafb1b68eab44c5b9640536c3cca",
"git_remote" : "https://x-access-token:ghs_TvmsZK2VAagFhHAuts3ZIuMFP8c1Ta1GVjOj@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-18-g3e2efbe"
"git_commit" : "a63bf1179fff7e98e7210310cef76ca8b16de00b",
"git_remote" : "https://x-access-token:ghs_6N7Ultp8C9GkfreyQPnww6yM2mslG21FIeb6@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-21-ga63bf11"
},
"package_config" : {
"name" : "demultiplex",
@@ -3054,7 +3054,7 @@ include { publish } from "${meta.resources_dir}/../../nextflow/io/publish/main.n
def date = new Date().format('yyyyMMdd_hhmmss')
def viash_config = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() + "/_viash.yaml"
def version = get_version(file(viash_config).text)
def version = get_version(viash_config)
workflow run_wf {
take:
@@ -3111,15 +3111,12 @@ workflow run_wf {
output_ch
}
def get_version(txt) {
matcher = txt =~ /(?m)^version:\s+(.*)$/
if (matcher.size() == 0) {
println("No version found, setting version to 'unknown_version'")
return "unknown_version"
} else {
println("Version found: ${matcher[0][1]}")
return matcher[0][1]
}
def get_version(inputFile) {
def yamlSlurper = new groovy.yaml.YamlSlurper()
def loaded_viash_config = yamlSlurper.parse(file(inputFile))
def version = (loaded_viash_config.version) ? loaded_viash_config.version : "unknown_version"
println("Version to be used: ${version}")
return version
}
// inner workflow hook