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Build branch v0.3 with version v0.3.0 (4947872)

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Build pipeline: viash-hub.craftbox.v0.3-s7x9q

Source commit: 4947872a1c

Source message: Bump version to v0.3.0
This commit is contained in:
CI
2025-08-28 13:25:24 +00:00
commit 4804ec8254
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198
target/executable/check_disk_space/.config.vsh.yaml Normal file
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name: "check_disk_space"
version: "v0.3.0"
argument_groups:
- name: "Inputs"
arguments:
- type: "integer"
name: "--tmp_space_required"
description: "Temporary space required in MB."
info: null
default:
- 1000
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--publish_space_required"
description: "Publish space required in MB."
info: null
default:
- 500
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--publish_dir"
description: "Directory where workflow outputs will be published."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
description: "Output file containing system resources details."
info: null
default:
- "output.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Check for available disk space on the system.\n\nThis component is only\
\ useful when working with persistent storage environments\nwhere all workflow steps\
\ execute on the same instance or share the same\nstorage volume. That is, running\
\ thus component on e.g. AWS Batch or\nother cloud-based systems will not work as\
\ expected, since each step\ncan run on a different instance and resources will\
\ not be shared.\n\nFor distributed environments, consider integrating resource\
\ checks directly\ninto the components that will actually consume the storage, rather\
\ than\nusing this standalone check.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
license: "MIT"
links:
repository: "https://github.com/viash-hub/craftbox"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "bash:latest"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.0"
namespace_separator: "/"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/check_disk_space/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/check_disk_space"
executable: "target/executable/check_disk_space/check_disk_space"
viash_version: "0.9.4"
git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
git_remote: "https://github.com/viash-hub/craftbox"
git_tag: "v0.1.0-9-g4947872"
package_config:
name: "craftbox"
version: "v0.3.0"
summary: "A collection of custom-tailored scripts and applied utilities built with\
\ Viash.\n"
description: "`craftbox` is a curated collection of custom scripts and utilities\
\ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
\ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
\ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
\ Ready:** Components are built to run directly via the command line or be smoothly\
\ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
\ scripts and tools developed for particular tasks that may not be found in broader\
\ collections.\n* **High Quality Standards (promoted by Viash):**\n * Clear\
\ documentation for components and their parameters.\n * Full exposure of underlying\
\ script/tool arguments for fine-grained control.\n * Containerized (Docker)\
\ to ensure dependency management and a consistent, reproducible runtime environment.\n\
\ * Unit tested where applicable to ensure components function as expected.\n"
info: null
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
keywords:
- "scripts"
- "custom"
- "implementations"
- "utilities"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/craftbox"
issue_tracker: "https://github.com/viash-hub/craftbox/issues"

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name: "concat_text"
version: "v0.3.0"
authors:
- name: "Toni Verbeiren"
roles:
- "author"
- "maintainer"
info:
links:
github: "tverbeiren"
linkedin: "verbeiren"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist and CEO"
- name: "Dries Schaumont"
roles:
- "reviewer"
info:
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Input arguments"
arguments:
- type: "file"
name: "--input"
description: "A list of (gzipped) text files."
info: null
example:
- "input?.txt.gz"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- name: "Output arguments"
arguments:
- type: "boolean_true"
name: "--gzip_output"
description: "Should the output be zipped?"
info: null
direction: "input"
- type: "file"
name: "--output"
description: "File to write the output to, optionally gzipped."
info: null
example:
- "output.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
summary: "Concatenate a number of text files"
description: "Concatenate a number of text files, handle gzipped text files gracefully\
\ and\noptionally gzip the output text file.\n\nThis component is useful for concatening\
\ fastq files from different lanes, for instance.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info:
improvements: "This component could be improved in 2 ways:\n 1. Allow for a mix\
\ of zipped and plain input files\n 2. Allow to specify a compression algorithm\
\ for the output\n"
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
license: "MIT"
links:
repository: "https://github.com/viash-hub/craftbox"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "alpine:latest"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.0"
namespace_separator: "/"
setup:
- type: "apk"
packages:
- "bash"
- "procps"
- "file"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/concat_text/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/concat_text"
executable: "target/executable/concat_text/concat_text"
viash_version: "0.9.4"
git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
git_remote: "https://github.com/viash-hub/craftbox"
git_tag: "v0.1.0-9-g4947872"
package_config:
name: "craftbox"
version: "v0.3.0"
summary: "A collection of custom-tailored scripts and applied utilities built with\
\ Viash.\n"
description: "`craftbox` is a curated collection of custom scripts and utilities\
\ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
\ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
\ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
\ Ready:** Components are built to run directly via the command line or be smoothly\
\ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
\ scripts and tools developed for particular tasks that may not be found in broader\
\ collections.\n* **High Quality Standards (promoted by Viash):**\n * Clear\
\ documentation for components and their parameters.\n * Full exposure of underlying\
\ script/tool arguments for fine-grained control.\n * Containerized (Docker)\
\ to ensure dependency management and a consistent, reproducible runtime environment.\n\
\ * Unit tested where applicable to ensure components function as expected.\n"
info: null
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
keywords:
- "scripts"
- "custom"
- "implementations"
- "utilities"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/craftbox"
issue_tracker: "https://github.com/viash-hub/craftbox/issues"

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298
target/executable/csv2fasta/.config.vsh.yaml Normal file
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name: "csv2fasta"
version: "v0.3.0"
authors:
- name: "Dries Schaumont"
roles:
- "author"
- "maintainer"
info:
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
- name: "Robrecht Cannoodt"
roles:
- "reviewer"
info:
links:
email: "robrecht@data-intuitive.com"
github: "rcannood"
orcid: "0000-0003-3641-729X"
linkedin: "robrechtcannoodt"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Science Engineer"
- name: "Open Problems"
href: "https://openproblems.bio"
role: "Core Member"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--input"
description: "CSV file to be processed."
info: null
example:
- "barcodes.csv"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--header"
description: "Parse the first line of the CSV file as a header.\n"
info: null
direction: "input"
- name: "CSV dialect options"
description: "Options that can be used to override the automatically detected\n\
dialect of the CSV file.\n"
arguments:
- type: "string"
name: "--delimiter"
description: "Overwrite the column delimiter character.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--quote_character"
description: "Overwrite the character used to denote the start and end of a quoted\
\ item.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "CSV column arguments"
description: "Parameters for the selection of columns from the CSV file.\nOnly required\
\ when your CSV file contains more than 2 columns,\notherwise the first column\
\ will be used for the FASTA header\nand the second for the FASTA nucleotide sequences.\
\ This default\ncan still be overwritten by using the options below.\n"
arguments:
- type: "string"
name: "--sequence_column"
description: "Name of the column containing the sequences. Implies 'header'.\n\
Cannot be used together with 'sequence_column_index'.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--name_column"
description: "Name of the column describing the FASTA headers. Implies 'header'.\n\
Cannot be used together with 'name_column_index'.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--sequence_column_index"
description: "Index of the column to use as the FASTA sequences, counter from\
\ the left and\nstarting from 0. Cannot be used in combination with the 'sequence_column'\
\ argument.\n"
info: null
required: false
min: 0
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--name_column_index"
description: "Index of the column to use as the FASTA headers, counter from the\
\ left and\nstarting from 0. Cannot be used in combination with 'name_column'.\n"
info: null
required: false
min: 0
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
description: "Output fasta file."
info: null
example:
- "barcodes.fasta"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "python_script"
path: "script.py"
is_executable: true
summary: "Convert a CSV file to FASTA entries"
description: "Convert two columns from a CSV file to FASTA entries. The CSV file can\n\
contain an optional header and each row (other than the header) becomes\na single\
\ FASTA record. One of the two columns will be used as the names\nfor the FASTA\
\ entries, while the other become the sequences. The sequences\ncolumn must only\
\ contain characters that are valid IUPAC notation for \nnucleotides or a group\
\ thereof (wildcard characters).\n"
test_resources:
- type: "python_script"
path: "test_csv2fasta.py"
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
license: "MIT"
links:
repository: "https://github.com/viash-hub/craftbox"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "python:slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.0"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "procps"
interactive: false
- type: "python"
user: false
packages:
- "dnaio"
upgrade: true
test_setup:
- type: "python"
user: false
packages:
- "pytest"
- "viashpy"
upgrade: true
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/csv2fasta/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/csv2fasta"
executable: "target/executable/csv2fasta/csv2fasta"
viash_version: "0.9.4"
git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
git_remote: "https://github.com/viash-hub/craftbox"
git_tag: "v0.1.0-9-g4947872"
package_config:
name: "craftbox"
version: "v0.3.0"
summary: "A collection of custom-tailored scripts and applied utilities built with\
\ Viash.\n"
description: "`craftbox` is a curated collection of custom scripts and utilities\
\ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
\ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
\ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
\ Ready:** Components are built to run directly via the command line or be smoothly\
\ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
\ scripts and tools developed for particular tasks that may not be found in broader\
\ collections.\n* **High Quality Standards (promoted by Viash):**\n * Clear\
\ documentation for components and their parameters.\n * Full exposure of underlying\
\ script/tool arguments for fine-grained control.\n * Containerized (Docker)\
\ to ensure dependency management and a consistent, reproducible runtime environment.\n\
\ * Unit tested where applicable to ensure components function as expected.\n"
info: null
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
keywords:
- "scripts"
- "custom"
- "implementations"
- "utilities"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/craftbox"
issue_tracker: "https://github.com/viash-hub/craftbox/issues"

1372
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194
target/executable/move_files_to_directory/.config.vsh.yaml Normal file
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name: "move_files_to_directory"
version: "v0.3.0"
authors:
- name: "Dorien Roosen"
roles:
- "maintainer"
info:
links:
email: "dorien@data-intuitive.com"
github: "dorien-er"
linkedin: "dorien-roosen"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Arguments"
arguments:
- type: "file"
name: "--input"
description: "Paths of the files that will be copied into the output directory."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--output"
description: "Path to output directory"
info: null
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--keep_symbolic_links"
alternatives:
- "-d"
description: "Preserve symbolic links."
info: null
direction: "input"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
summary: "Publish one or multiple files to the same directory"
description: "This component copies one or multiple files to the same destination\
\ directory, creating the output directory if it doesn't exist."
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
license: "MIT"
links:
repository: "https://github.com/viash-hub/craftbox"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "debian:latest"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.0"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "procps"
interactive: false
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/move_files_to_directory/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/move_files_to_directory"
executable: "target/executable/move_files_to_directory/move_files_to_directory"
viash_version: "0.9.4"
git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
git_remote: "https://github.com/viash-hub/craftbox"
git_tag: "v0.1.0-9-g4947872"
package_config:
name: "craftbox"
version: "v0.3.0"
summary: "A collection of custom-tailored scripts and applied utilities built with\
\ Viash.\n"
description: "`craftbox` is a curated collection of custom scripts and utilities\
\ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
\ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
\ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
\ Ready:** Components are built to run directly via the command line or be smoothly\
\ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
\ scripts and tools developed for particular tasks that may not be found in broader\
\ collections.\n* **High Quality Standards (promoted by Viash):**\n * Clear\
\ documentation for components and their parameters.\n * Full exposure of underlying\
\ script/tool arguments for fine-grained control.\n * Containerized (Docker)\
\ to ensure dependency management and a consistent, reproducible runtime environment.\n\
\ * Unit tested where applicable to ensure components function as expected.\n"
info: null
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
keywords:
- "scripts"
- "custom"
- "implementations"
- "utilities"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/craftbox"
issue_tracker: "https://github.com/viash-hub/craftbox/issues"

1188
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238
target/executable/sync_resources/.config.vsh.yaml Normal file
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@@ -0,0 +1,238 @@
name: "sync_resources"
version: "v0.3.0"
authors:
- name: "Robrecht Cannoodt"
roles:
- "author"
- "maintainer"
info:
links:
email: "robrecht@data-intuitive.com"
github: "rcannood"
orcid: "0000-0003-3641-729X"
linkedin: "robrechtcannoodt"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Science Engineer"
- name: "Open Problems"
href: "https://openproblems.bio"
role: "Core Member"
- name: "Dries Schaumont"
roles:
- "reviewer"
info:
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--input"
alternatives:
- "-i"
description: "Path to the _viash.yaml project configuration file."
info: null
default:
- "_viash.yaml"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
alternatives:
- "-o"
description: "Path to the directory where the resources will be synced to."
info: null
default:
- "."
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Arguments"
arguments:
- type: "boolean_true"
name: "--dryrun"
description: "Does not display the operations performed from the specified command."
info: null
direction: "input"
- type: "string"
name: "--exclude"
description: "Exclude all files or objects from the command that matches the specified\
\ pattern."
info: null
required: false
direction: "input"
multiple: true
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
summary: "Sync a Viash package's test resources to the local filesystem"
description: "Sync a Viash package's test resources to the local filesystem based\
\ on the\nthe `.info.test_resources` field in the `_viash.yaml` file. This is useful\
\ for\ntesting and debugging purposes.\n"
usage: "sync_resources\nsync_resources --input _viash.yaml --output .\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
license: "MIT"
links:
repository: "https://github.com/viash-hub/craftbox"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "alpine:3"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.0"
namespace_separator: "/"
setup:
- type: "apk"
packages:
- "bash"
- "rclone"
- "yq"
- type: "docker"
run:
- "rclone config create s3 s3 anonymous=true"
- "rclone config create gs gcs anonymous=true"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/sync_resources/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/sync_resources"
executable: "target/executable/sync_resources/sync_resources"
viash_version: "0.9.4"
git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
git_remote: "https://github.com/viash-hub/craftbox"
git_tag: "v0.1.0-9-g4947872"
package_config:
name: "craftbox"
version: "v0.3.0"
summary: "A collection of custom-tailored scripts and applied utilities built with\
\ Viash.\n"
description: "`craftbox` is a curated collection of custom scripts and utilities\
\ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
\ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
\ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
\ Ready:** Components are built to run directly via the command line or be smoothly\
\ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
\ scripts and tools developed for particular tasks that may not be found in broader\
\ collections.\n* **High Quality Standards (promoted by Viash):**\n * Clear\
\ documentation for components and their parameters.\n * Full exposure of underlying\
\ script/tool arguments for fine-grained control.\n * Containerized (Docker)\
\ to ensure dependency management and a consistent, reproducible runtime environment.\n\
\ * Unit tested where applicable to ensure components function as expected.\n"
info: null
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
keywords:
- "scripts"
- "custom"
- "implementations"
- "utilities"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/craftbox"
issue_tracker: "https://github.com/viash-hub/craftbox/issues"

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target/executable/untar/.config.vsh.yaml Normal file
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@@ -0,0 +1,223 @@
name: "untar"
version: "v0.3.0"
authors:
- name: "Dries Schaumont"
roles:
- "author"
- "maintainer"
info:
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
- name: "Robrecht Cannoodt"
roles:
- "reviewer"
info:
links:
email: "robrecht@data-intuitive.com"
github: "rcannood"
orcid: "0000-0003-3641-729X"
linkedin: "robrechtcannoodt"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Science Engineer"
- name: "Open Problems"
href: "https://openproblems.bio"
role: "Core Member"
argument_groups:
- name: "Input arguments"
arguments:
- type: "file"
name: "--input"
description: "Tarball file to be unpacked."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output arguments"
arguments:
- type: "file"
name: "--output"
description: "Directory to write the contents of the .tar file to."
info: null
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Other arguments"
arguments:
- type: "string"
name: "--exclude"
alternatives:
- "-e"
description: "Prevents any file or member whose name matches the shell wildcard\
\ (pattern) from being extracted."
info: null
example:
- "docs/figures"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
summary: "Unpack a .tar file"
description: "Unpack a .tar file. When the contents of the .tar file is just a single\
\ directory,\nput the contents of the directory into the output folder instead of\
\ that directory.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
license: "MIT"
links:
repository: "https://github.com/viash-hub/craftbox"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.0"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "procps"
interactive: false
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/untar/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/untar"
executable: "target/executable/untar/untar"
viash_version: "0.9.4"
git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
git_remote: "https://github.com/viash-hub/craftbox"
git_tag: "v0.1.0-9-g4947872"
package_config:
name: "craftbox"
version: "v0.3.0"
summary: "A collection of custom-tailored scripts and applied utilities built with\
\ Viash.\n"
description: "`craftbox` is a curated collection of custom scripts and utilities\
\ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
\ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
\ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
\ Ready:** Components are built to run directly via the command line or be smoothly\
\ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
\ scripts and tools developed for particular tasks that may not be found in broader\
\ collections.\n* **High Quality Standards (promoted by Viash):**\n * Clear\
\ documentation for components and their parameters.\n * Full exposure of underlying\
\ script/tool arguments for fine-grained control.\n * Containerized (Docker)\
\ to ensure dependency management and a consistent, reproducible runtime environment.\n\
\ * Unit tested where applicable to ensure components function as expected.\n"
info: null
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.0'"
keywords:
- "scripts"
- "custom"
- "implementations"
- "utilities"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/craftbox"
issue_tracker: "https://github.com/viash-hub/craftbox/issues"

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