vsh/toolbox
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Build branch main with version main (69c4536)

Browse Source 
Build pipeline: viash-hub.toolbox.main-5vhb4

Source commit: 69c4536b84

Source message: Remove package version from main branch (#14)

* remove package version from main branch

* update ci
This commit is contained in:
CI
2025-05-06 20:32:04 +00:00
parent 36b9c79457
commit 932beffdb5
12 changed files with 51 additions and 52 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
_viash.yaml
View File

@@ -1,5 +1,4 @@
name: toolbox
version: v0.1.0
summary: |
A collection of curated command-line tools for general IT tasks, built with Viash.
description: |

2
nextflow.config
View File

@@ -1,6 +1,6 @@
manifest {
name = "toolbox"
version = "v0.1.0"
version = "main"
defaultBranch = "main"
nextflowVersion = "!>=20.12.1-edge"
}

10
target/executable/bgzip/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "bgzip"
version: "v0.1.0"
version: "main"
argument_groups:
- name: "Inputs"
arguments:
@@ -210,7 +210,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/htslib:1.19--h81da01d_0"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -228,11 +228,11 @@ build_info:
output: "target/executable/bgzip"
executable: "target/executable/bgzip/bgzip"
viash_version: "0.9.4"
git_commit: "d33eb370683ba1f1132ec7d7b6884c8040dc901a"
git_commit: "69c4536b849c9a776972a12162376f824b4b4504"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"
version: "v0.1.0"
version: "main"
summary: "A collection of curated command-line tools for general IT tasks, built\
\ with Viash.\n"
description: "`toolbox` provides a versatile suite of IT components, following the\
@@ -255,7 +255,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "toolbox"
- "command-line"

14
target/executable/bgzip/bgzip
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# bgzip v0.1.0
# bgzip main
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -448,10 +448,10 @@ ENTRYPOINT []
RUN bgzip -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/bgzip: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component bgzip"
LABEL org.opencontainers.image.created="2025-05-06T20:10:22Z"
LABEL org.opencontainers.image.created="2025-05-06T20:26:42Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/htslib"
LABEL org.opencontainers.image.revision="d33eb370683ba1f1132ec7d7b6884c8040dc901a"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="69c4536b849c9a776972a12162376f824b4b4504"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
fi
@@ -568,7 +568,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bgzip v0.1.0"
echo "bgzip main"
echo ""
echo "Block compression/decompression utility"
echo ""
@@ -674,7 +674,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "bgzip v0.1.0"
echo "bgzip main"
exit
;;
--input)
@@ -910,7 +910,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/bgzip:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/bgzip:main'
fi
# print dockerfile

10
target/executable/yq/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "yq"
version: "v0.1.0"
version: "main"
argument_groups:
- name: "Inputs"
arguments:
@@ -237,7 +237,7 @@ engines:
id: "docker"
image: "alpine:latest"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apk"
@@ -258,11 +258,11 @@ build_info:
output: "target/executable/yq"
executable: "target/executable/yq/yq"
viash_version: "0.9.4"
git_commit: "d33eb370683ba1f1132ec7d7b6884c8040dc901a"
git_commit: "69c4536b849c9a776972a12162376f824b4b4504"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"
version: "v0.1.0"
version: "main"
summary: "A collection of curated command-line tools for general IT tasks, built\
\ with Viash.\n"
description: "`toolbox` provides a versatile suite of IT components, following the\
@@ -285,7 +285,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "toolbox"
- "command-line"

14
target/executable/yq/yq
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# yq v0.1.0
# yq main
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apk add --no-cache bash yq-go
RUN /usr/bin/yq --version | sed 's/.*version\sv\(.*\)/yq: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component yq"
LABEL org.opencontainers.image.created="2025-05-06T20:10:22Z"
LABEL org.opencontainers.image.created="2025-05-06T20:26:42Z"
LABEL org.opencontainers.image.source="https://github.com/mikefarah/yq"
LABEL org.opencontainers.image.revision="d33eb370683ba1f1132ec7d7b6884c8040dc901a"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="69c4536b849c9a776972a12162376f824b4b4504"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "yq v0.1.0"
echo "yq main"
echo ""
echo "A portable YAML, JSON, XML, CSV, TOML and properties processor"
echo ""
@@ -659,7 +659,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "yq v0.1.0"
echo "yq main"
exit
;;
--input)
@@ -844,7 +844,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/yq:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/yq:main'
fi
# print dockerfile

10
target/nextflow/bgzip/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "bgzip"
version: "v0.1.0"
version: "main"
argument_groups:
- name: "Inputs"
arguments:
@@ -210,7 +210,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/htslib:1.19--h81da01d_0"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -228,11 +228,11 @@ build_info:
output: "target/nextflow/bgzip"
executable: "target/nextflow/bgzip/main.nf"
viash_version: "0.9.4"
git_commit: "d33eb370683ba1f1132ec7d7b6884c8040dc901a"
git_commit: "69c4536b849c9a776972a12162376f824b4b4504"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"
version: "v0.1.0"
version: "main"
summary: "A collection of curated command-line tools for general IT tasks, built\
\ with Viash.\n"
description: "`toolbox` provides a versatile suite of IT components, following the\
@@ -255,7 +255,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "toolbox"
- "command-line"

14
target/nextflow/bgzip/main.nf
View File

@@ -1,4 +1,4 @@
// bgzip v0.1.0
// bgzip main
//
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "bgzip",
"version" : "v0.1.0",
"version" : "main",
"argument_groups" : [
{
"name" : "Inputs",
@@ -3295,7 +3295,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/htslib:1.19--h81da01d_0",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3317,12 +3317,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/bgzip",
"viash_version" : "0.9.4",
"git_commit" : "d33eb370683ba1f1132ec7d7b6884c8040dc901a",
"git_commit" : "69c4536b849c9a776972a12162376f824b4b4504",
"git_remote" : "https://github.com/viash-hub/toolbox"
},
"package_config" : {
"name" : "toolbox",
"version" : "v0.1.0",
"version" : "main",
"summary" : "A collection of curated command-line tools for general IT tasks, built with Viash.\n",
"description" : "`toolbox` provides a versatile suite of IT components, following the robust Viash (https://viash.io) framework.\nThis package focuses on delivering reliable, standalone tools that can be easily integrated into larger computational workflows.\n\nThe core philosophy emphasizes **reusability**, **reproducibility**, and adherence to **best practices** in component creation. Key features of `toolbox` components include:\n\n* **Standalone & Nextflow Ready:** Execute components directly from the command line or seamlessly incorporate them into Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation for each component and its parameters.\n * Full exposure of the underlying tool's arguments for maximum flexibility.\n * Containerized (Docker) to ensure consistent environments and manage dependencies, leading to enhanced reproducibility.\n * Unit tested to verify functionality and ensure reliability.\n",
"viash_version" : "0.9.4",
@@ -3332,7 +3332,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.1.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"toolbox",
@@ -3795,7 +3795,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/toolbox/bgzip",
"tag" : "v0.1.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/nextflow/bgzip/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'bgzip'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'main'
description = 'Block compression/decompression utility'
}

10
target/nextflow/yq/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "yq"
version: "v0.1.0"
version: "main"
argument_groups:
- name: "Inputs"
arguments:
@@ -237,7 +237,7 @@ engines:
id: "docker"
image: "alpine:latest"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apk"
@@ -258,11 +258,11 @@ build_info:
output: "target/nextflow/yq"
executable: "target/nextflow/yq/main.nf"
viash_version: "0.9.4"
git_commit: "d33eb370683ba1f1132ec7d7b6884c8040dc901a"
git_commit: "69c4536b849c9a776972a12162376f824b4b4504"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"
version: "v0.1.0"
version: "main"
summary: "A collection of curated command-line tools for general IT tasks, built\
\ with Viash.\n"
description: "`toolbox` provides a versatile suite of IT components, following the\
@@ -285,7 +285,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "toolbox"
- "command-line"

14
target/nextflow/yq/main.nf
View File

@@ -1,4 +1,4 @@
// yq v0.1.0
// yq main
//
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "yq",
"version" : "v0.1.0",
"version" : "main",
"argument_groups" : [
{
"name" : "Inputs",
@@ -3301,7 +3301,7 @@ meta = [
"id" : "docker",
"image" : "alpine:latest",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3330,12 +3330,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/yq",
"viash_version" : "0.9.4",
"git_commit" : "d33eb370683ba1f1132ec7d7b6884c8040dc901a",
"git_commit" : "69c4536b849c9a776972a12162376f824b4b4504",
"git_remote" : "https://github.com/viash-hub/toolbox"
},
"package_config" : {
"name" : "toolbox",
"version" : "v0.1.0",
"version" : "main",
"summary" : "A collection of curated command-line tools for general IT tasks, built with Viash.\n",
"description" : "`toolbox` provides a versatile suite of IT components, following the robust Viash (https://viash.io) framework.\nThis package focuses on delivering reliable, standalone tools that can be easily integrated into larger computational workflows.\n\nThe core philosophy emphasizes **reusability**, **reproducibility**, and adherence to **best practices** in component creation. Key features of `toolbox` components include:\n\n* **Standalone & Nextflow Ready:** Execute components directly from the command line or seamlessly incorporate them into Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation for each component and its parameters.\n * Full exposure of the underlying tool's arguments for maximum flexibility.\n * Containerized (Docker) to ensure consistent environments and manage dependencies, leading to enhanced reproducibility.\n * Unit tested to verify functionality and ensure reliability.\n",
"viash_version" : "0.9.4",
@@ -3345,7 +3345,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.1.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"toolbox",
@@ -3792,7 +3792,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/toolbox/yq",
"tag" : "v0.1.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/nextflow/yq/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'yq'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'main'
description = 'A portable YAML, JSON, XML, CSV, TOML and properties processor'
}