CI
879926dac6
Build pipeline: viash-hub.htrnaseq.update-resources-2j4gn
Source commit: f1f0c98bba
Source message: Merge branch 'main' into update-resources
197 lines
8.6 KiB
JSON
197 lines
8.6 KiB
JSON
{
|
|
"$schema": "http://json-schema.org/draft-07/schema",
|
|
"title": "parallel_map",
|
|
"description": "Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n",
|
|
"type": "object",
|
|
"definitions": {
|
|
|
|
|
|
|
|
"input arguments" : {
|
|
"title": "Input arguments",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"input_r1": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: List of `file`, required, multiple_sep: `\";\"`. Input FASTQ files for the forward reads",
|
|
"help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Input FASTQ files for the forward reads. All FASTQ file names must start with the prefix \u0027{well_id}_R1\u0027, where\n\u0027well_id\u0027 can be found as the sequence identifier in the barcodes FASTA file (see \u0027barcodesFasta\u0027 argument).\nFor each FASTQ file, a matching FASTQ file for the reverse reads must be provided to the \u0027input_r2\u0027 argument,\nmeaning that their \u0027well_id\u0027 prefix must match. The number of items provided for \u0027input_r1\u0027 must be equal\nto the number of items for \u0027input_r2\u0027.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"input_r2": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: List of `file`, required, multiple_sep: `\";\"`. Input FASTQ files for the reverse reads",
|
|
"help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Input FASTQ files for the reverse reads. All FASTQ file names must start with the prefix \u0027{well_id}_R2\u0027, where\n\u0027well_id\u0027 can be found as the sequence identifier in the barcodes FASTA file (see \u0027barcodesFasta\u0027 argument).\nFor each FASTQ file, a matching FASTQ file for the reverse reads must be provided to the \u0027input_r1\u0027 argument,\nmeaning that their \u0027well_id\u0027 prefix must match. The number of items provided for \u0027input_r1\u0027 must be equal\nto the number of items for \u0027input_r2\u0027.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"genomeDir": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, required. Reference genome to match to",
|
|
"help_text": "Type: `file`, required. Reference genome to match to. Can be generated from genomic FASTA sequences and a genome annotation\nby using STAR with \u0027--runMode genomeGenerate\u0027.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"barcodesFasta": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, required. FASTA file where each entry specifies a unique barcode sequence present at the start of the forward input reads\n(input_r1)",
|
|
"help_text": "Type: `file`, required. FASTA file where each entry specifies a unique barcode sequence present at the start of the forward input reads\n(input_r1). The IDs of each barcode (the start of the FASTA headers up until the first whitespace character) must\nmatch with the start of one input FASTQ pair.\n"
|
|
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"barcode arguments" : {
|
|
"title": "Barcode arguments",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"umiLength": {
|
|
"type":
|
|
"integer",
|
|
"description": "Type: `integer`, required. Length of the Unique Molecular Identifiers (UMI)",
|
|
"help_text": "Type: `integer`, required. Length of the Unique Molecular Identifiers (UMI). The UMI are expected to be located after the barcodes in the\nforwards reads.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"limitBAMsortRAM": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, default: `10000000000`. ",
|
|
"help_text": "Type: `string`, default: `10000000000`. "
|
|
,
|
|
"default":"10000000000"
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"runtime arguments" : {
|
|
"title": "Runtime arguments",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"runThreadN": {
|
|
"type":
|
|
"integer",
|
|
"description": "Type: `integer`, default: `1`. Number of threads to use for a single STAR execution",
|
|
"help_text": "Type: `integer`, default: `1`. Number of threads to use for a single STAR execution."
|
|
,
|
|
"default":1
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"output arguments" : {
|
|
"title": "Output arguments",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"output": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: List of `file`, required, default: `./*`, multiple_sep: `\";\"`. A list of output folders which are the result of using STAR to map each input FASTQ pair STAR to the reference genome",
|
|
"help_text": "Type: List of `file`, required, default: `./*`, multiple_sep: `\";\"`. A list of output folders which are the result of using STAR to map each input FASTQ pair STAR to the reference genome.\nThe order of the items DO NOT match with the order of the entries in the barcodes FASTA file or the input FASTQ pairs. \n"
|
|
,
|
|
"default":"./*"
|
|
}
|
|
|
|
|
|
,
|
|
"joblog": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, default: `execution_log.txt`. Where to store the log file listing all the jobs",
|
|
"help_text": "Type: `file`, default: `execution_log.txt`. Where to store the log file listing all the jobs."
|
|
,
|
|
"default":"execution_log.txt"
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"nextflow input-output arguments" : {
|
|
"title": "Nextflow input-output arguments",
|
|
"type": "object",
|
|
"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.",
|
|
"properties": {
|
|
|
|
|
|
"publish_dir": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
|
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"param_list": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
|
|
"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.",
|
|
"hidden": true
|
|
|
|
}
|
|
|
|
|
|
}
|
|
}
|
|
},
|
|
"allOf": [
|
|
|
|
{
|
|
"$ref": "#/definitions/input arguments"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/barcode arguments"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/runtime arguments"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/output arguments"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|