CI
b533a32bc8
Build pipeline: vsh-ci-template-7m7cc
Source commit: 73b07a96e0
Source message: Fix quotes in test (#4)
* Fix quotes in test
* query the first output file to pick up the 'name' value again and output it
grep with start and end position constaints
165 lines
6.3 KiB
JSON
165 lines
6.3 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "yq",
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"description": "A portable YAML, JSON, XML, CSV, TOML and properties processor",
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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. files to be processed",
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"help_text": "Type: `file`, required. files to be processed"
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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.$key.output.output`. output file",
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"help_text": "Type: `file`, required, default: `$id.$key.output.output`. output file"
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,
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"default": "$id.$key.output.output"
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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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"eval": {
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"type":
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"string",
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"description": "Type: `string`, required. expression to evaluate",
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"help_text": "Type: `string`, required. expression to evaluate"
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}
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,
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"indent": {
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"type":
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"integer",
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"description": "Type: `integer`. sets indent level for output (default 2)",
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"help_text": "Type: `integer`. sets indent level for output (default 2)"
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}
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,
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"input_format": {
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"type":
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"string",
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"description": "Type: `string`, choices: ``auto`, `a`, `yaml`, `y`, `json`, `j`, `props`, `p`, `csv`, `c`, `tsv`, `t`, `xml`, `x`, `base64`, `uri`, `toml`, `shell`, `s`, `lua`, `l``. parse format for input",
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"help_text": "Type: `string`, choices: ``auto`, `a`, `yaml`, `y`, `json`, `j`, `props`, `p`, `csv`, `c`, `tsv`, `t`, `xml`, `x`, `base64`, `uri`, `toml`, `shell`, `s`, `lua`, `l``. parse format for input. (default \"auto\")",
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"enum": ["auto", "a", "yaml", "y", "json", "j", "props", "p", "csv", "c", "tsv", "t", "xml", "x", "base64", "uri", "toml", "shell", "s", "lua", "l"]
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}
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,
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"output_format": {
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"type":
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"string",
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"description": "Type: `string`, choices: ``auto`, `a`, `yaml`, `y`, `json`, `j`, `props`, `p`, `csv`, `c`, `tsv`, `t`, `xml`, `x`, `base64`, `uri`, `toml`, `shell`, `s`, `lua`, `l``. output format type",
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"help_text": "Type: `string`, choices: ``auto`, `a`, `yaml`, `y`, `json`, `j`, `props`, `p`, `csv`, `c`, `tsv`, `t`, `xml`, `x`, `base64`, `uri`, `toml`, `shell`, `s`, `lua`, `l``. output format type. (default \"auto\")",
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"enum": ["auto", "a", "yaml", "y", "json", "j", "props", "p", "csv", "c", "tsv", "t", "xml", "x", "base64", "uri", "toml", "shell", "s", "lua", "l"]
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}
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,
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"pretty_print": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. pretty print, shorthand for \u0027",
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"help_text": "Type: `boolean_true`, default: `false`. pretty print, shorthand for \u0027... style = \"\"\u0027"
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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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