CI
c439638095
Build pipeline: viash-hub.htrnaseq.unpack-genome-5zk5c
Source commit: 7c0705a514
Source message: Add ability to unpack input genome
207 lines
7.2 KiB
JSON
207 lines
7.2 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "parallel_map",
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"description": "Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n",
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"type": "object",
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"definitions": {
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"input arguments" : {
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"title": "Input 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: List of `file`, required, multiple_sep: `\":\"`. ",
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"help_text": "Type: List of `file`, required, multiple_sep: `\":\"`. "
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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: List of `file`, required, multiple_sep: `\":\"`. ",
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"help_text": "Type: List of `file`, required, multiple_sep: `\":\"`. "
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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. STAR reference directory",
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"help_text": "Type: `file`, required. STAR reference directory"
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}
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,
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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: `\":\"`. The barcodes/wells to process",
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"help_text": "Type: List of `string`, required, multiple_sep: `\":\"`. The barcodes/wells to process"
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}
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}
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},
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"barcode arguments" : {
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"title": "Barcode arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"wellBarcodesLength": {
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"type":
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"integer",
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"description": "Type: `integer`, required. The length of the well barcodes",
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"help_text": "Type: `integer`, required. The length of the well barcodes"
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}
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,
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"umiLength": {
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"type":
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"integer",
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"description": "Type: `integer`, required. The length of the UMIs",
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"help_text": "Type: `integer`, required. The length of the UMIs"
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}
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,
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"limitBAMsortRAM": {
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"type":
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"string",
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"description": "Type: `string`, default: `10000000000`. ",
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"help_text": "Type: `string`, default: `10000000000`. "
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,
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"default": "10000000000"
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}
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}
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},
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"runtime arguments" : {
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"title": "Runtime arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"runThreadN": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `1`. Number of threads to use for a single STAR execution",
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"help_text": "Type: `integer`, default: `1`. Number of threads to use for a single STAR execution."
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,
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"default": "1"
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}
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}
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},
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"output arguments" : {
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"title": "Output arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"output": {
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"type":
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"string",
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"description": "Type: List of `file`, required, default: `$id.$key.output_*./*`, multiple_sep: `\":\"`. Location of the output folders, 1 folder per barcode",
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"help_text": "Type: List of `file`, required, default: `$id.$key.output_*./*`, multiple_sep: `\":\"`. Location of the output folders, 1 folder per barcode. The value used\nfor this argument must contain a \u0027*\u0027, which will be replaced with the\nbarcode to form the final output location for that barcode.\n"
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,
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"default": "$id.$key.output_*./*"
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}
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,
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"joblog": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.joblog.txt`. Where to store the log file listing all the jobs",
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"help_text": "Type: `file`, default: `$id.$key.joblog.txt`. Where to store the log file listing all the jobs."
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,
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"default": "$id.$key.joblog.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/input arguments"
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},
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{
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"$ref": "#/definitions/barcode arguments"
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},
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{
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"$ref": "#/definitions/runtime arguments"
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},
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{
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"$ref": "#/definitions/output arguments"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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