CI
47c9784250
Build pipeline: viash-hub.biobox.v0.3-cl68g
Source commit: d86bd5cf62
Source message: Merge remote-tracking branch 'origin/main' into v0.3
161 lines
5.8 KiB
JSON
161 lines
5.8 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "fq_subsample",
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"description": "fq subsample outputs a subset of records from single or paired FASTQ files.",
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"type": "object",
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"definitions": {
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"input" : {
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"title": "Input",
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"type": "object",
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"description": "No description",
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"properties": {
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"input_1": {
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"type":
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"string",
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"description": "Type: `file`, required. First input fastq file to subsample",
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"help_text": "Type: `file`, required. First input fastq file to subsample. Accepts both raw and gzipped FASTQ inputs."
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}
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,
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"input_2": {
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"type":
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"string",
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"description": "Type: `file`. Second input fastq files to subsample",
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"help_text": "Type: `file`. Second input fastq files to subsample. Accepts both raw and gzipped FASTQ inputs."
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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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"output_1": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files",
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"help_text": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`."
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,
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"default":"$id.$key.output_1.output_1"
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}
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,
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"output_2": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files",
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"help_text": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`."
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,
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"default":"$id.$key.output_2.output_2"
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}
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}
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},
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"options" : {
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"title": "Options",
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"type": "object",
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"description": "No description",
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"properties": {
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"probability": {
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"type":
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"number",
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"description": "Type: `double`. The probability a record is kept, as a percentage (0",
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"help_text": "Type: `double`. The probability a record is kept, as a percentage (0.0, 1.0). Cannot be used with `record-count`"
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}
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,
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"record_count": {
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"type":
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"integer",
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"description": "Type: `integer`. The exact number of records to keep",
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"help_text": "Type: `integer`. The exact number of records to keep. Cannot be used with `probability`"
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}
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,
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"seed": {
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"type":
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"integer",
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"description": "Type: `integer`. Seed to use for the random number generator",
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"help_text": "Type: `integer`. Seed to use for the random number generator"
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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"
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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/options"
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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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