CI
5cb3251eaf
Build pipeline: viash-hub.toolbox.v0.1.x-fphr8
Source commit: 2c07979559
Source message: Merge remote-tracking branch 'origin/main' into v0.1.x
217 lines
7.4 KiB
JSON
217 lines
7.4 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "bgzip",
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"description": "Block compression/decompression utility",
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"type": "object",
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"definitions": {
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"inputs" : {
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"title": "Inputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"input": {
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"type":
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"string",
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"description": "Type: `file`, required. file to be compressed or decompressed",
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"help_text": "Type: `file`, required. file to be compressed or decompressed"
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}
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}
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},
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"outputs" : {
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"title": "Outputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"output": {
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"type":
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"string",
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"description": "Type: `file`, required, default: `$id.$key.output`. compressed or decompressed output",
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"help_text": "Type: `file`, required, default: `$id.$key.output`. compressed or decompressed output"
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,
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"default":"$id.$key.output"
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}
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,
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"index_name": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.index_name`. name of BGZF index file [file",
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"help_text": "Type: `file`, default: `$id.$key.index_name`. name of BGZF index file [file.gz.gzi]"
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,
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"default":"$id.$key.index_name"
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}
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}
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},
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"arguments" : {
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"title": "Arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"offset": {
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"type":
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"integer",
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"description": "Type: `integer`. decompress at virtual file pointer (0-based uncompressed offset)",
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"help_text": "Type: `integer`. decompress at virtual file pointer (0-based uncompressed offset)"
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}
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,
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"decompress": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. decompress the input file",
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"help_text": "Type: `boolean_true`, default: `false`. decompress the input file"
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,
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"default":false
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}
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,
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"rebgzip": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. use an index file to bgzip a file",
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"help_text": "Type: `boolean_true`, default: `false`. use an index file to bgzip a file"
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,
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"default":false
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}
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,
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"index": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. compress and create BGZF index",
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"help_text": "Type: `boolean_true`, default: `false`. compress and create BGZF index"
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,
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"default":false
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}
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,
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"compress_level": {
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"type":
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"integer",
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"description": "Type: `integer`. compression level to use when compressing; 0 to 9, or -1 for default [-1]",
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"help_text": "Type: `integer`. compression level to use when compressing; 0 to 9, or -1 for default [-1]"
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}
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,
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"reindex": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. (re)index the output file",
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"help_text": "Type: `boolean_true`, default: `false`. (re)index the output file"
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,
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"default":false
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}
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,
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"size": {
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"type":
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"integer",
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"description": "Type: `integer`. decompress INT bytes (uncompressed size)",
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"help_text": "Type: `integer`. decompress INT bytes (uncompressed size)"
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}
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,
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"test": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. test integrity of compressed file",
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"help_text": "Type: `boolean_true`, default: `false`. test integrity of compressed file"
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,
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"default":false
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}
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,
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"binary": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Don\u0027t align blocks with text lines",
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"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t align blocks with text lines"
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,
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"default":false
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}
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}
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},
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"nextflow input-output arguments" : {
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"title": "Nextflow input-output arguments",
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"type": "object",
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"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.",
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"properties": {
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"publish_dir": {
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"type":
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"string",
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"description": "Type: `string`, required, example: `output/`. Path to an output directory",
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"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
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}
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,
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"param_list": {
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"type":
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"string",
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"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
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"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.",
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"hidden": true
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/definitions/inputs"
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},
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{
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"$ref": "#/definitions/outputs"
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},
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{
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"$ref": "#/definitions/arguments"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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