CI
bde35f120c
Build pipeline: viash-hub.htrnaseq.main-48gzk
Source commit: b98f6367d6
Source message: Add BAM statistics calculations on pool and well level (#6)
122 lines
4.7 KiB
JSON
122 lines
4.7 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "parallel_map_wf",
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"description": "Map RNA sequencing data, provided as fastq files (paired-end) to a reference genome using STAR Solo.\nInput data must have been demultiplexed beforehand, meaning that a single fastq pair provides data for\none barcode (one well). Multiple wells can be mapped in parallel by providing multiple events to the \nworkflow. Output is provided as mapped output per pool, i.e. one output is provided per pool.xx\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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"input_r1": {
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"type":
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"string",
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"description": "Type: `file`, required. ",
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"help_text": "Type: `file`, required. "
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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. ",
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"help_text": "Type: `file`, required. "
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}
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,
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"barcode": {
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"type":
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"string",
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"description": "Type: `string`, required. ",
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"help_text": "Type: `string`, required. "
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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. ",
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"help_text": "Type: `string`, required. "
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}
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,
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"genomeDir": {
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"type":
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"string",
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"description": "Type: `file`, required. ",
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"help_text": "Type: `file`, required. "
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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`, required, default: `$id.$key.output.output`. ",
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"help_text": "Type: `file`, required, default: `$id.$key.output.output`. "
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,
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"default": "$id.$key.output.output"
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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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