CI
e7f74d0239
Build pipeline: viash-hub.craftbox.publish-fz2zz
Source commit: e6f7cf2cfc
Source message: update changelog
107 lines
4.5 KiB
JSON
107 lines
4.5 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "concat_text",
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"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",
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"type": "object",
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"definitions": {
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"input arguments" : {
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"title": "Input arguments",
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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: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\";\"`. A list of (gzipped) text files",
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"help_text": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\";\"`. A list of (gzipped) text files."
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}
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}
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},
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"output arguments" : {
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"title": "Output arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"gzip_output": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Should the output be zipped?",
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"help_text": "Type: `boolean_true`, default: `false`. Should the output be zipped?"
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,
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"default":false
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}
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,
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"output": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output.txt`, example: `output.txt`. File to write the output to, optionally gzipped",
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"help_text": "Type: `file`, default: `$id.$key.output.txt`, example: `output.txt`. File to write the output to, optionally gzipped."
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,
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"default":"$id.$key.output.txt"
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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/input arguments"
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},
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{
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"$ref": "#/definitions/output arguments"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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