Build branch main with version main (9ca16ea)
Build pipeline: viash-hub.craftbox.main-q45l7
Source commit: 9ca16ea58d
Source message: add publish component (#10)
* add publish component
* update changleog
* update changelog
* address pr comments
* update test
* Update src/move_files_to_directory/config.vsh.yaml
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
* Update CHANGELOG.md
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
---------
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
This commit is contained in:
@@ -4,6 +4,8 @@
|
||||
|
||||
* `sync_resources`: Sync a Viash package's test resources to the local filesystem (PR #7).
|
||||
|
||||
* `move_files_to_directory`: Publish one or multiple files to an output directory (PR #10).
|
||||
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||||
## MINOR CHANGES
|
||||
|
||||
* Add documentation to multiple components (PR #9).
|
||||
|
||||
35
src/move_files_to_directory/config.vsh.yaml
Normal file
35
src/move_files_to_directory/config.vsh.yaml
Normal file
@@ -0,0 +1,35 @@
|
||||
name: move_files_to_directory
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||||
summary: Publish one or multiple files to the same directory
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||||
description: This component copies one or multiple files to the same destination directory, creating the output directory if it doesn't exist.
|
||||
authors:
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||||
- __merge__: /src/_authors/dorien_roosen.yaml
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||||
roles: [ maintainer ]
|
||||
arguments:
|
||||
- name: "--input"
|
||||
type: file
|
||||
direction: input
|
||||
required: true
|
||||
multiple: true
|
||||
description: Paths of the files that will be copied into the output directory.
|
||||
- name: "--output"
|
||||
type: file
|
||||
direction: output
|
||||
required: true
|
||||
description: Path to output directory
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||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
|
||||
engines:
|
||||
- type: docker
|
||||
image: debian:latest
|
||||
setup:
|
||||
- type: apt
|
||||
packages: [procps]
|
||||
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
25
src/move_files_to_directory/script.sh
Normal file
25
src/move_files_to_directory/script.sh
Normal file
@@ -0,0 +1,25 @@
|
||||
#!/bin/bash
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||||
|
||||
set -eo pipefail
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||||
|
||||
## VIASH START
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||||
par_input="input.txt;input_2.txt"
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||||
par_output="output"
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||||
## VIASH END
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||||
|
||||
|
||||
if [[ ! -d "$par_output" ]]; then
|
||||
mkdir -p "$par_output"
|
||||
fi
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||||
|
||||
# Process multiple input files
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||||
IFS=";" read -ra input_files <<< "$par_input"
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for file in "${input_files[@]}"; do
|
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# Check if the file exists before copying
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if [[ -f "$file" ]]; then
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cp "$file" "$par_output/"
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echo "Copied $file to $par_output/"
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||||
else
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||||
echo "Warning: Input file $file does not exist, skipping"
|
||||
fi
|
||||
done
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||||
22
src/move_files_to_directory/test.sh
Normal file
22
src/move_files_to_directory/test.sh
Normal file
@@ -0,0 +1,22 @@
|
||||
#!/usr/bin/env bash
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set -ex
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||||
|
||||
# create temporary directory and clean up on exit
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||||
TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX")
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||||
function clean_up {
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[[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
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||||
}
|
||||
trap clean_up EXIT
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touch "$TMPDIR/test_file.txt"
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touch "$TMPDIR/another_file.txt"
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./move_files_to_directory \
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--input "$TMPDIR/test_file.txt" \
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--input "$TMPDIR/another_file.txt" \
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--output "$TMPDIR/test_output"
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|
||||
[[ ! -d "$TMPDIR/test_output" ]] && echo "It seems no output directory is generated" && exit 1
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[[ ! -f "$TMPDIR/test_output/test_file.txt" ]] && [[ ! -f test_output/another_file.txt ]] && echo "Output files were not copied to the output directory" && exit 1
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|
||||
echo ">> Test succeeded!"
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||||
@@ -175,9 +175,9 @@ build_info:
|
||||
output: "target/executable/concat_text"
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||||
executable: "target/executable/concat_text/concat_text"
|
||||
viash_version: "0.9.3"
|
||||
git_commit: "8f9353f15e4d6952eca57e896f962a60b42b0a3c"
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||||
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
git_tag: "v0.1.0-4-g8f9353f"
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git_tag: "v0.1.0-5-g9ca16ea"
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||||
package_config:
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||||
name: "craftbox"
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||||
version: "main"
|
||||
|
||||
@@ -453,9 +453,9 @@ RUN apk add --no-cache bash procps file
|
||||
|
||||
LABEL org.opencontainers.image.authors="Toni Verbeiren, Dries Schaumont"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component concat_text"
|
||||
LABEL org.opencontainers.image.created="2025-04-08T07:49:55Z"
|
||||
LABEL org.opencontainers.image.created="2025-05-02T09:33:23Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
|
||||
LABEL org.opencontainers.image.revision="8f9353f15e4d6952eca57e896f962a60b42b0a3c"
|
||||
LABEL org.opencontainers.image.revision="9ca16ea58d5f010e31714265802c016280594624"
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||||
LABEL org.opencontainers.image.version="main"
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||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -257,9 +257,9 @@ build_info:
|
||||
output: "target/executable/csv2fasta"
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||||
executable: "target/executable/csv2fasta/csv2fasta"
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||||
viash_version: "0.9.3"
|
||||
git_commit: "8f9353f15e4d6952eca57e896f962a60b42b0a3c"
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||||
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
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||||
git_remote: "https://github.com/viash-hub/craftbox"
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||||
git_tag: "v0.1.0-4-g8f9353f"
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||||
git_tag: "v0.1.0-5-g9ca16ea"
|
||||
package_config:
|
||||
name: "craftbox"
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version: "main"
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||||
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@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
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|
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LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component csv2fasta"
|
||||
LABEL org.opencontainers.image.created="2025-04-08T07:49:56Z"
|
||||
LABEL org.opencontainers.image.created="2025-05-02T09:33:24Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
|
||||
LABEL org.opencontainers.image.revision="8f9353f15e4d6952eca57e896f962a60b42b0a3c"
|
||||
LABEL org.opencontainers.image.revision="9ca16ea58d5f010e31714265802c016280594624"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
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||||
|
||||
173
target/executable/move_files_to_directory/.config.vsh.yaml
Normal file
173
target/executable/move_files_to_directory/.config.vsh.yaml
Normal file
@@ -0,0 +1,173 @@
|
||||
name: "move_files_to_directory"
|
||||
version: "main"
|
||||
authors:
|
||||
- name: "Dorien Roosen"
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||||
roles:
|
||||
- "maintainer"
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||||
info:
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||||
links:
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||||
email: "dorien@data-intuitive.com"
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||||
github: "dorien-er"
|
||||
linkedin: "dorien-roosen"
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||||
organizations:
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||||
- name: "Data Intuitive"
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||||
href: "https://www.data-intuitive.com"
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||||
role: "Data Scientist"
|
||||
argument_groups:
|
||||
- name: "Arguments"
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||||
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
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||||
required: true
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||||
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: ";"
|
||||
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\
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||||
\ directory, creating the output directory if it doesn't exist."
|
||||
test_resources:
|
||||
- type: "bash_script"
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||||
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: "main"
|
||||
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: "0.9.3"
|
||||
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
git_tag: "v0.1.0-5-g9ca16ea"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "main"
|
||||
description: "A collection of custom-tailored scripts and applied tools.\n"
|
||||
info: null
|
||||
viash_version: "0.9.3"
|
||||
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 := 'main'"
|
||||
keywords:
|
||||
- "scripts"
|
||||
- "custom"
|
||||
- "implementations"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/craftbox"
|
||||
issue_tracker: "https://github.com/viash-hub/craftbox/issues"
|
||||
1155
target/executable/move_files_to_directory/move_files_to_directory
Executable file
1155
target/executable/move_files_to_directory/move_files_to_directory
Executable file
File diff suppressed because it is too large
Load Diff
@@ -197,9 +197,9 @@ build_info:
|
||||
output: "target/executable/sync_resources"
|
||||
executable: "target/executable/sync_resources/sync_resources"
|
||||
viash_version: "0.9.3"
|
||||
git_commit: "8f9353f15e4d6952eca57e896f962a60b42b0a3c"
|
||||
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
git_tag: "v0.1.0-4-g8f9353f"
|
||||
git_tag: "v0.1.0-5-g9ca16ea"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "main"
|
||||
|
||||
@@ -455,9 +455,9 @@ RUN rclone config create s3 s3 anonymous=true
|
||||
RUN rclone config create gs gcs anonymous=true
|
||||
LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Dries Schaumont"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component sync_resources"
|
||||
LABEL org.opencontainers.image.created="2025-04-08T07:49:55Z"
|
||||
LABEL org.opencontainers.image.created="2025-05-02T09:33:24Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
|
||||
LABEL org.opencontainers.image.revision="8f9353f15e4d6952eca57e896f962a60b42b0a3c"
|
||||
LABEL org.opencontainers.image.revision="9ca16ea58d5f010e31714265802c016280594624"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -182,9 +182,9 @@ build_info:
|
||||
output: "target/executable/untar"
|
||||
executable: "target/executable/untar/untar"
|
||||
viash_version: "0.9.3"
|
||||
git_commit: "8f9353f15e4d6952eca57e896f962a60b42b0a3c"
|
||||
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
git_tag: "v0.1.0-4-g8f9353f"
|
||||
git_tag: "v0.1.0-5-g9ca16ea"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "main"
|
||||
|
||||
@@ -455,9 +455,9 @@ RUN apt-get update && \
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component untar"
|
||||
LABEL org.opencontainers.image.created="2025-04-08T07:49:56Z"
|
||||
LABEL org.opencontainers.image.created="2025-05-02T09:33:23Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
|
||||
LABEL org.opencontainers.image.revision="8f9353f15e4d6952eca57e896f962a60b42b0a3c"
|
||||
LABEL org.opencontainers.image.revision="9ca16ea58d5f010e31714265802c016280594624"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -175,9 +175,9 @@ build_info:
|
||||
output: "target/nextflow/concat_text"
|
||||
executable: "target/nextflow/concat_text/main.nf"
|
||||
viash_version: "0.9.3"
|
||||
git_commit: "8f9353f15e4d6952eca57e896f962a60b42b0a3c"
|
||||
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
git_tag: "v0.1.0-4-g8f9353f"
|
||||
git_tag: "v0.1.0-5-g9ca16ea"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "main"
|
||||
|
||||
@@ -3267,9 +3267,9 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/concat_text",
|
||||
"viash_version" : "0.9.3",
|
||||
"git_commit" : "8f9353f15e4d6952eca57e896f962a60b42b0a3c",
|
||||
"git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
|
||||
"git_remote" : "https://github.com/viash-hub/craftbox",
|
||||
"git_tag" : "v0.1.0-4-g8f9353f"
|
||||
"git_tag" : "v0.1.0-5-g9ca16ea"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "craftbox",
|
||||
|
||||
@@ -257,9 +257,9 @@ build_info:
|
||||
output: "target/nextflow/csv2fasta"
|
||||
executable: "target/nextflow/csv2fasta/main.nf"
|
||||
viash_version: "0.9.3"
|
||||
git_commit: "8f9353f15e4d6952eca57e896f962a60b42b0a3c"
|
||||
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
git_tag: "v0.1.0-4-g8f9353f"
|
||||
git_tag: "v0.1.0-5-g9ca16ea"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "main"
|
||||
|
||||
@@ -3357,9 +3357,9 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/csv2fasta",
|
||||
"viash_version" : "0.9.3",
|
||||
"git_commit" : "8f9353f15e4d6952eca57e896f962a60b42b0a3c",
|
||||
"git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
|
||||
"git_remote" : "https://github.com/viash-hub/craftbox",
|
||||
"git_tag" : "v0.1.0-4-g8f9353f"
|
||||
"git_tag" : "v0.1.0-5-g9ca16ea"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "craftbox",
|
||||
|
||||
173
target/nextflow/move_files_to_directory/.config.vsh.yaml
Normal file
173
target/nextflow/move_files_to_directory/.config.vsh.yaml
Normal file
@@ -0,0 +1,173 @@
|
||||
name: "move_files_to_directory"
|
||||
version: "main"
|
||||
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: ";"
|
||||
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: "main"
|
||||
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: "nextflow"
|
||||
engine: "docker|native"
|
||||
output: "target/nextflow/move_files_to_directory"
|
||||
executable: "target/nextflow/move_files_to_directory/main.nf"
|
||||
viash_version: "0.9.3"
|
||||
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
git_tag: "v0.1.0-5-g9ca16ea"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "main"
|
||||
description: "A collection of custom-tailored scripts and applied tools.\n"
|
||||
info: null
|
||||
viash_version: "0.9.3"
|
||||
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 := 'main'"
|
||||
keywords:
|
||||
- "scripts"
|
||||
- "custom"
|
||||
- "implementations"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/craftbox"
|
||||
issue_tracker: "https://github.com/viash-hub/craftbox/issues"
|
||||
3814
target/nextflow/move_files_to_directory/main.nf
Normal file
3814
target/nextflow/move_files_to_directory/main.nf
Normal file
File diff suppressed because it is too large
Load Diff
126
target/nextflow/move_files_to_directory/nextflow.config
Normal file
126
target/nextflow/move_files_to_directory/nextflow.config
Normal file
@@ -0,0 +1,126 @@
|
||||
manifest {
|
||||
name = 'move_files_to_directory'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'main'
|
||||
description = 'This component copies one or multiple files to the same destination directory, creating the output directory if it doesn\'t exist.'
|
||||
author = 'Dorien Roosen'
|
||||
}
|
||||
|
||||
process.container = 'nextflow/bash:latest'
|
||||
|
||||
// detect tempdir
|
||||
tempDir = java.nio.file.Paths.get(
|
||||
System.getenv('NXF_TEMP') ?:
|
||||
System.getenv('VIASH_TEMP') ?:
|
||||
System.getenv('TEMPDIR') ?:
|
||||
System.getenv('TMPDIR') ?:
|
||||
'/tmp'
|
||||
).toAbsolutePath()
|
||||
|
||||
profiles {
|
||||
no_publish {
|
||||
process {
|
||||
withName: '.*' {
|
||||
publishDir = [
|
||||
enabled: false
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
mount_temp {
|
||||
docker.temp = tempDir
|
||||
podman.temp = tempDir
|
||||
charliecloud.temp = tempDir
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
// docker.userEmulation = true
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
docker.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
podman {
|
||||
podman.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
shifter {
|
||||
shifter.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
charliecloud {
|
||||
charliecloud.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
}
|
||||
}
|
||||
|
||||
process{
|
||||
withLabel: mem1gb { memory = 1000000000.B }
|
||||
withLabel: mem2gb { memory = 2000000000.B }
|
||||
withLabel: mem5gb { memory = 5000000000.B }
|
||||
withLabel: mem10gb { memory = 10000000000.B }
|
||||
withLabel: mem20gb { memory = 20000000000.B }
|
||||
withLabel: mem50gb { memory = 50000000000.B }
|
||||
withLabel: mem100gb { memory = 100000000000.B }
|
||||
withLabel: mem200gb { memory = 200000000000.B }
|
||||
withLabel: mem500gb { memory = 500000000000.B }
|
||||
withLabel: mem1tb { memory = 1000000000000.B }
|
||||
withLabel: mem2tb { memory = 2000000000000.B }
|
||||
withLabel: mem5tb { memory = 5000000000000.B }
|
||||
withLabel: mem10tb { memory = 10000000000000.B }
|
||||
withLabel: mem20tb { memory = 20000000000000.B }
|
||||
withLabel: mem50tb { memory = 50000000000000.B }
|
||||
withLabel: mem100tb { memory = 100000000000000.B }
|
||||
withLabel: mem200tb { memory = 200000000000000.B }
|
||||
withLabel: mem500tb { memory = 500000000000000.B }
|
||||
withLabel: mem1gib { memory = 1073741824.B }
|
||||
withLabel: mem2gib { memory = 2147483648.B }
|
||||
withLabel: mem4gib { memory = 4294967296.B }
|
||||
withLabel: mem8gib { memory = 8589934592.B }
|
||||
withLabel: mem16gib { memory = 17179869184.B }
|
||||
withLabel: mem32gib { memory = 34359738368.B }
|
||||
withLabel: mem64gib { memory = 68719476736.B }
|
||||
withLabel: mem128gib { memory = 137438953472.B }
|
||||
withLabel: mem256gib { memory = 274877906944.B }
|
||||
withLabel: mem512gib { memory = 549755813888.B }
|
||||
withLabel: mem1tib { memory = 1099511627776.B }
|
||||
withLabel: mem2tib { memory = 2199023255552.B }
|
||||
withLabel: mem4tib { memory = 4398046511104.B }
|
||||
withLabel: mem8tib { memory = 8796093022208.B }
|
||||
withLabel: mem16tib { memory = 17592186044416.B }
|
||||
withLabel: mem32tib { memory = 35184372088832.B }
|
||||
withLabel: mem64tib { memory = 70368744177664.B }
|
||||
withLabel: mem128tib { memory = 140737488355328.B }
|
||||
withLabel: mem256tib { memory = 281474976710656.B }
|
||||
withLabel: mem512tib { memory = 562949953421312.B }
|
||||
withLabel: cpu1 { cpus = 1 }
|
||||
withLabel: cpu2 { cpus = 2 }
|
||||
withLabel: cpu5 { cpus = 5 }
|
||||
withLabel: cpu10 { cpus = 10 }
|
||||
withLabel: cpu20 { cpus = 20 }
|
||||
withLabel: cpu50 { cpus = 50 }
|
||||
withLabel: cpu100 { cpus = 100 }
|
||||
withLabel: cpu200 { cpus = 200 }
|
||||
withLabel: cpu500 { cpus = 500 }
|
||||
withLabel: cpu1000 { cpus = 1000 }
|
||||
}
|
||||
|
||||
|
||||
81
target/nextflow/move_files_to_directory/nextflow_schema.json
Normal file
81
target/nextflow/move_files_to_directory/nextflow_schema.json
Normal file
@@ -0,0 +1,81 @@
|
||||
{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "move_files_to_directory",
|
||||
"description": "This component copies one or multiple files to the same destination directory, creating the output directory if it doesn\u0027t exist.",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
|
||||
"arguments" : {
|
||||
"title": "Arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"input": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: List of `file`, required, multiple_sep: `\";\"`. Paths of the files that will be copied into the output directory",
|
||||
"help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Paths of the files that will be copied into the output directory."
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, default: `$id.$key.output`. Path to output directory",
|
||||
"help_text": "Type: `file`, required, default: `$id.$key.output`. Path to output directory"
|
||||
,
|
||||
"default":"$id.$key.output"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"nextflow input-output arguments" : {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
|
||||
"properties": {
|
||||
|
||||
|
||||
"publish_dir": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
||||
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"param_list": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
|
||||
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
|
||||
"hidden": true
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/arguments"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -197,9 +197,9 @@ build_info:
|
||||
output: "target/nextflow/sync_resources"
|
||||
executable: "target/nextflow/sync_resources/main.nf"
|
||||
viash_version: "0.9.3"
|
||||
git_commit: "8f9353f15e4d6952eca57e896f962a60b42b0a3c"
|
||||
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
git_tag: "v0.1.0-4-g8f9353f"
|
||||
git_tag: "v0.1.0-5-g9ca16ea"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "main"
|
||||
|
||||
@@ -3299,9 +3299,9 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/sync_resources",
|
||||
"viash_version" : "0.9.3",
|
||||
"git_commit" : "8f9353f15e4d6952eca57e896f962a60b42b0a3c",
|
||||
"git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
|
||||
"git_remote" : "https://github.com/viash-hub/craftbox",
|
||||
"git_tag" : "v0.1.0-4-g8f9353f"
|
||||
"git_tag" : "v0.1.0-5-g9ca16ea"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "craftbox",
|
||||
|
||||
@@ -38,10 +38,10 @@
|
||||
"output": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, default: `$id.$key.output.output`. Path to the directory where the resources will be synced to",
|
||||
"help_text": "Type: `file`, default: `$id.$key.output.output`. Path to the directory where the resources will be synced to."
|
||||
"description": "Type: `file`, default: `.`. Path to the directory where the resources will be synced to",
|
||||
"help_text": "Type: `file`, default: `.`. Path to the directory where the resources will be synced to."
|
||||
,
|
||||
"default":"$id.$key.output.output"
|
||||
"default":"."
|
||||
}
|
||||
|
||||
|
||||
|
||||
@@ -182,9 +182,9 @@ build_info:
|
||||
output: "target/nextflow/untar"
|
||||
executable: "target/nextflow/untar/main.nf"
|
||||
viash_version: "0.9.3"
|
||||
git_commit: "8f9353f15e4d6952eca57e896f962a60b42b0a3c"
|
||||
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
git_tag: "v0.1.0-4-g8f9353f"
|
||||
git_tag: "v0.1.0-5-g9ca16ea"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "main"
|
||||
|
||||
@@ -3278,9 +3278,9 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/untar",
|
||||
"viash_version" : "0.9.3",
|
||||
"git_commit" : "8f9353f15e4d6952eca57e896f962a60b42b0a3c",
|
||||
"git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
|
||||
"git_remote" : "https://github.com/viash-hub/craftbox",
|
||||
"git_tag" : "v0.1.0-4-g8f9353f"
|
||||
"git_tag" : "v0.1.0-5-g9ca16ea"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "craftbox",
|
||||
|
||||
@@ -37,10 +37,10 @@
|
||||
"output": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, default: `$id.$key.output.output`. Directory to write the contents of the ",
|
||||
"help_text": "Type: `file`, required, default: `$id.$key.output.output`. Directory to write the contents of the .tar file to."
|
||||
"description": "Type: `file`, required, default: `$id.$key.output`. Directory to write the contents of the ",
|
||||
"help_text": "Type: `file`, required, default: `$id.$key.output`. Directory to write the contents of the .tar file to."
|
||||
,
|
||||
"default":"$id.$key.output.output"
|
||||
"default":"$id.$key.output"
|
||||
}
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user