CI
a95268a2b5
Build pipeline: viash-hub.htrnaseq.main-mjsqg
Source commit: cb58990a33
Source message: Fix create_report build after R update (#52)
92 lines
4.3 KiB
JSON
92 lines
4.3 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "create_pdata",
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"description": "Create a pdata file by combining the mapping statistics \n",
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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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"star_stats_file": {
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"type":
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"string",
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"description": "Type: `file`, required. Tab-delimited text file containing statistics (per column) that were generated\nfrom the STAR log files (Log",
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"help_text": "Type: `file`, required. Tab-delimited text file containing statistics (per column) that were generated\nfrom the STAR log files (Log.final.out, Summary.csv, ReadsPerGene.out.tab).\nEach entry (row) in the file describes the values for one well (barcode).\n"
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}
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,
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"nrReadsNrGenesPerChromPool": {
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"type":
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"string",
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"description": "Type: `file`, required. Pivot table in tsv format of the combined nrReadsNrGenesPerChrom files from STAR",
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"help_text": "Type: `file`, required. Pivot table in tsv format of the combined nrReadsNrGenesPerChrom files from STAR. \nDescribes per chromosome (as columns) the number of reads, as well as the total number \nof reads per cell barcode and the percentage of nuclear, ERCC and mitochondrial\nreads.\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: `pData.$id.txt`. ",
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"help_text": "Type: `file`, default: `pData.$id.txt`. "
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,
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"default":"pData.$id.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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