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Build branch main with version main (7cec5ca)

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Build pipeline: viash-hub.toolbox.main-g4l8f

Source commit: 7cec5cac69

Source message: Merge pull request #10 from viash-hub/bump_viash_to_0_9_0_rc_7

Bump viash to 0.9.0-RC7
This commit is contained in:
CI
2024-08-19 07:36:43 +00:00
parent abe5837cb5
commit e3aee2f8b4
13 changed files with 54 additions and 19 deletions
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8
CHANGELOG.md
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@@ -1,5 +1,13 @@
# toolbox unreleased
## MINOR CHANGES
* Updated the test CI (PR #6).
* Bump viash to 0.9.0-RC7 (PR #10).
# toolbox v0.1.0
## NEW FEATURES
* `bgzip`: Add bgzip functionality to compress and decompress files (initial commit).

2
README.md
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@@ -9,7 +9,7 @@ License](https://img.shields.io/github/license/viash-hub/toolbox.png)](https://g
[![GitHub
Issues](https://img.shields.io/github/issues/viash-hub/toolbox.png)](https://github.com/viash-hub/toolbox/issues)
[![Viash
version](https://img.shields.io/badge/Viash-v0.9.0--RC6-blue)](https://viash.io)
version](https://img.shields.io/badge/Viash-v0.9.0--RC7-blue)](https://viash.io)
A collection of command-line tools.

2
_viash.yaml
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@@ -7,7 +7,7 @@ links:
issue_tracker: https://github.com/viash-hub/toolbox/issues
repository: https://github.com/viash-hub/toolbox
viash_version: 0.9.0-RC6
viash_version: 0.9.0-RC7
config_mods: |
.requirements.commands := ['ps']

3
src/yq/config.vsh.yaml
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@@ -16,6 +16,7 @@ argument_groups:
direction: input
description: files to be processed
required: true
example: input.yaml
- name: Outputs
arguments:
- name: --output
@@ -23,12 +24,14 @@ argument_groups:
direction: output
description: output file
required: true
example: output.yaml
- name: Arguments
arguments:
- name: --eval
type: string
description: expression to evaluate
required: true
example: '.name = "foo"'
- name: --indent
type: integer
description: sets indent level for output (default 2)

2
target/executable/bgzip/.config.vsh.yaml
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@@ -225,7 +225,7 @@ build_info:
output: "target/executable/bgzip"
executable: "target/executable/bgzip/bgzip"
viash_version: "0.9.0-RC6"
git_commit: "3eff836ca92b6e13debba8436ad5a484790f8c90"
git_commit: "7cec5cac6937b310c9f172d4c5655a5f20d2442f"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"

4
target/executable/bgzip/bgzip
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@@ -508,9 +508,9 @@ 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="2024-07-01T09:02:42Z"
LABEL org.opencontainers.image.created="2024-08-19T07:32:49Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/htslib"
LABEL org.opencontainers.image.revision="3eff836ca92b6e13debba8436ad5a484790f8c90"
LABEL org.opencontainers.image.revision="7cec5cac6937b310c9f172d4c5655a5f20d2442f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

8
target/executable/yq/.config.vsh.yaml
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@@ -7,6 +7,8 @@ argument_groups:
name: "--input"
description: "files to be processed"
info: null
example:
- "input.yaml"
must_exist: true
create_parent: true
required: true
@@ -19,6 +21,8 @@ argument_groups:
name: "--output"
description: "output file"
info: null
example:
- "output.yaml"
must_exist: true
create_parent: true
required: true
@@ -31,6 +35,8 @@ argument_groups:
name: "--eval"
description: "expression to evaluate"
info: null
example:
- ".name = \"foo\""
required: true
direction: "input"
multiple: false
@@ -249,7 +255,7 @@ build_info:
output: "target/executable/yq"
executable: "target/executable/yq/yq"
viash_version: "0.9.0-RC6"
git_commit: "3eff836ca92b6e13debba8436ad5a484790f8c90"
git_commit: "7cec5cac6937b310c9f172d4c5655a5f20d2442f"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"

7
target/executable/yq/yq
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@@ -178,16 +178,19 @@ function ViashHelp {
echo "Inputs:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " example: input.yaml"
echo " files to be processed"
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: output.yaml"
echo " output file"
echo ""
echo "Arguments:"
echo " --eval"
echo " type: string, required parameter"
echo " example: .name = \"foo\""
echo " expression to evaluate"
echo ""
echo " -I, --indent"
@@ -490,9 +493,9 @@ 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="2024-07-01T09:02:43Z"
LABEL org.opencontainers.image.created="2024-08-19T07:32:48Z"
LABEL org.opencontainers.image.source="https://github.com/mikefarah/yq"
LABEL org.opencontainers.image.revision="3eff836ca92b6e13debba8436ad5a484790f8c90"
LABEL org.opencontainers.image.revision="7cec5cac6937b310c9f172d4c5655a5f20d2442f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/nextflow/bgzip/.config.vsh.yaml
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@@ -225,7 +225,7 @@ build_info:
output: "target/nextflow/bgzip"
executable: "target/nextflow/bgzip/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "3eff836ca92b6e13debba8436ad5a484790f8c90"
git_commit: "7cec5cac6937b310c9f172d4c5655a5f20d2442f"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"

2
target/nextflow/bgzip/main.nf
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@@ -3061,7 +3061,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/bgzip",
"viash_version" : "0.9.0-RC6",
"git_commit" : "3eff836ca92b6e13debba8436ad5a484790f8c90",
"git_commit" : "7cec5cac6937b310c9f172d4c5655a5f20d2442f",
"git_remote" : "https://github.com/viash-hub/toolbox"
},
"package_config" : {

8
target/nextflow/yq/.config.vsh.yaml
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@@ -7,6 +7,8 @@ argument_groups:
name: "--input"
description: "files to be processed"
info: null
example:
- "input.yaml"
must_exist: true
create_parent: true
required: true
@@ -19,6 +21,8 @@ argument_groups:
name: "--output"
description: "output file"
info: null
example:
- "output.yaml"
must_exist: true
create_parent: true
required: true
@@ -31,6 +35,8 @@ argument_groups:
name: "--eval"
description: "expression to evaluate"
info: null
example:
- ".name = \"foo\""
required: true
direction: "input"
multiple: false
@@ -249,7 +255,7 @@ build_info:
output: "target/nextflow/yq"
executable: "target/nextflow/yq/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "3eff836ca92b6e13debba8436ad5a484790f8c90"
git_commit: "7cec5cac6937b310c9f172d4c5655a5f20d2442f"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"

11
target/nextflow/yq/main.nf
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@@ -2788,6 +2788,9 @@ meta = [
"type" : "file",
"name" : "--input",
"description" : "files to be processed",
"example" : [
"input.yaml"
],
"must_exist" : true,
"create_parent" : true,
"required" : true,
@@ -2804,6 +2807,9 @@ meta = [
"type" : "file",
"name" : "--output",
"description" : "output file",
"example" : [
"output.yaml"
],
"must_exist" : true,
"create_parent" : true,
"required" : true,
@@ -2820,6 +2826,9 @@ meta = [
"type" : "string",
"name" : "--eval",
"description" : "expression to evaluate",
"example" : [
".name = \\"foo\\""
],
"required" : true,
"direction" : "input",
"multiple" : false,
@@ -3065,7 +3074,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/yq",
"viash_version" : "0.9.0-RC6",
"git_commit" : "3eff836ca92b6e13debba8436ad5a484790f8c90",
"git_commit" : "7cec5cac6937b310c9f172d4c5655a5f20d2442f",
"git_remote" : "https://github.com/viash-hub/toolbox"
},
"package_config" : {

14
target/nextflow/yq/nextflow_schema.json
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@@ -17,8 +17,8 @@
"input": {
"type":
"string",
"description": "Type: `file`, required. files to be processed",
"help_text": "Type: `file`, required. files to be processed"
"description": "Type: `file`, required, example: `input.yaml`. files to be processed",
"help_text": "Type: `file`, required, example: `input.yaml`. files to be processed"
}
@@ -37,10 +37,10 @@
"output": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.output.output`. output file",
"help_text": "Type: `file`, required, default: `$id.$key.output.output`. output file"
"description": "Type: `file`, required, default: `$id.$key.output.yaml`, example: `output.yaml`. output file",
"help_text": "Type: `file`, required, default: `$id.$key.output.yaml`, example: `output.yaml`. output file"
,
"default": "$id.$key.output.output"
"default": "$id.$key.output.yaml"
}
@@ -58,8 +58,8 @@
"eval": {
"type":
"string",
"description": "Type: `string`, required. expression to evaluate",
"help_text": "Type: `string`, required. expression to evaluate"
"description": "Type: `string`, required, example: `.name = \"foo\"`. expression to evaluate",
"help_text": "Type: `string`, required, example: `.name = \"foo\"`. expression to evaluate"
}