CI
a95268a2b5
Build pipeline: viash-hub.htrnaseq.main-mjsqg
Source commit: cb58990a33
Source message: Fix create_report build after R update (#52)
112 lines
5.2 KiB
JSON
112 lines
5.2 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "combine_star_logs",
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"description": "No description",
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"type": "object",
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"definitions": {
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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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"barcodes": {
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"type":
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"string",
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"description": "Type: List of `string`, required, multiple_sep: `\";\"`. Barcodes responding to the respective log files",
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"help_text": "Type: List of `string`, required, multiple_sep: `\";\"`. Barcodes responding to the respective log files.\n"
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}
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,
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"star_logs": {
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"type":
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"string",
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"description": "Type: List of `file`, required, example: `Log.final.out`, multiple_sep: `\";\"`. Paths to the STAR log files (most frequently called Log",
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"help_text": "Type: List of `file`, required, example: `Log.final.out`, multiple_sep: `\";\"`. Paths to the STAR log files (most frequently called Log.final.out)\n"
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}
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,
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"gene_summary_logs": {
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"type":
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"string",
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"description": "Type: List of `file`, required, example: `Summary.txt`, multiple_sep: `\";\"`. Paths to the Summary",
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"help_text": "Type: List of `file`, required, example: `Summary.txt`, multiple_sep: `\";\"`. Paths to the Summary.csv files from the STAR Solo output. Can be found in\nthe \u0027Solo.out/Gene\u0027 folder relative to the root of the STAR output directory. \n"
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}
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,
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"reads_per_gene_logs": {
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"type":
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"string",
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"description": "Type: List of `file`, required, multiple_sep: `\";\"`. Paths to the \u0027ReadsPerGene",
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"help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Paths to the \u0027ReadsPerGene.out.tab\u0027 files as output by STAR.\n"
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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: `starLogs.txt`. Tab-delimited file describing for each barcode (as the rows), the metrics (as columns)\ngathered from the different input files",
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"help_text": "Type: `file`, default: `starLogs.txt`. Tab-delimited file describing for each barcode (as the rows), the metrics (as columns)\ngathered from the different input files. \n"
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,
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"default":"starLogs.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/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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