CI
044a3af7a9
Build pipeline: viash-hub.htrnaseq.main-n8w4c
Source commit: 21831c2104
Source message: Fix well_demultiplex test
147 lines
5.6 KiB
JSON
147 lines
5.6 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "groupWells",
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"description": "N/A\n",
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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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"well": {
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"type":
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"string",
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"description": "Type: `string`, required, example: `barcode_1`. Barcode identifier for a well",
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"help_text": "Type: `string`, required, example: `barcode_1`. Barcode identifier for a well"
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}
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,
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"pool": {
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"type":
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"string",
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"description": "Type: `string`, required, example: `pool_1`. Identifier of the pool",
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"help_text": "Type: `string`, required, example: `pool_1`. Identifier of the pool"
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}
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,
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"input_r1": {
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"type":
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"string",
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"description": "Type: `file`, required, example: `input.fastq.gz`. Path to the input for R1",
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"help_text": "Type: `file`, required, example: `input.fastq.gz`. Path to the input for R1"
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}
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,
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"input_r2": {
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"type":
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"string",
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"description": "Type: `file`, required, example: `input.fastq.gz`. Path to the input for R1",
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"help_text": "Type: `file`, required, example: `input.fastq.gz`. Path to the input for R1"
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}
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}
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},
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"output" : {
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"title": "Output",
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"type": "object",
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"description": "No description",
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"properties": {
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"wells": {
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"type":
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"string",
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"description": "Type: List of `string`, example: `input.fastq.gz`, multiple_sep: `\";\"`. List of grouped wells (by means of barcodes)",
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"help_text": "Type: List of `string`, example: `input.fastq.gz`, multiple_sep: `\";\"`. List of grouped wells (by means of barcodes)"
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}
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,
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"output_r1": {
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"type":
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"string",
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"description": "Type: List of `file`, default: `$id.$key.output_r1_*.output_r1_*`, multiple_sep: `\";\"`. Path to output for R2",
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"help_text": "Type: List of `file`, default: `$id.$key.output_r1_*.output_r1_*`, multiple_sep: `\";\"`. Path to output for R2"
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,
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"default": "$id.$key.output_r1_*.output_r1_*"
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}
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,
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"output_r2": {
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"type":
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"string",
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"description": "Type: List of `file`, default: `$id.$key.output_r2_*.output_r2_*`, multiple_sep: `\";\"`. Path to the output for R2",
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"help_text": "Type: List of `file`, default: `$id.$key.output_r2_*.output_r2_*`, multiple_sep: `\";\"`. Path to the output for R2"
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,
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"default": "$id.$key.output_r2_*.output_r2_*"
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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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"$ref": "#/definitions/output"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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