CI
14e0d12189
Build pipeline: viash-hub.rnaseq.main-b6jtr
Source commit: ce40a4a6d9
Source message: add unit tests
169 lines
5.9 KiB
JSON
169 lines
5.9 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "stringtie",
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"description": "Transcript assembly and quantification for RNA-Seq\n",
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"type": "object",
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"definitions": {
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"input" : {
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"title": "Input",
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"type": "object",
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"description": "No description",
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"properties": {
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"strandedness": {
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"type":
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"string",
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"description": "Type: `string`. Forward or reverse strand?",
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"help_text": "Type: `string`. Forward or reverse strand?"
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}
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,
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"bam": {
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"type":
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"string",
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"description": "Type: `file`. ",
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"help_text": "Type: `file`. "
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}
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,
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"annotation_gtf": {
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"type":
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"string",
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"description": "Type: `file`. ",
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"help_text": "Type: `file`. "
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}
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,
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"extra_stringtie_args": {
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"type":
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"string",
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"description": "Type: `string`. Extra arguments for running StringTie",
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"help_text": "Type: `string`. Extra arguments for running StringTie"
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}
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,
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"stringtie_ignore_gtf": {
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"type":
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"boolean",
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"description": "Type: `boolean`. Perform reference-guided de novo assembly of transcripts using StringTie, i",
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"help_text": "Type: `boolean`. Perform reference-guided de novo assembly of transcripts using StringTie, i.e. don\u0027t restrict to those in GTF file."
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}
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}
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},
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"output" : {
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"title": "Output",
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"type": "object",
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"description": "No description",
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"properties": {
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"transcript_gtf": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.transcript_gtf.gtf`. ",
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"help_text": "Type: `file`, default: `$id.$key.transcript_gtf.gtf`. "
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,
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"default":"$id.$key.transcript_gtf.gtf"
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}
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,
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"coverage_gtf": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.coverage_gtf.gtf`. ",
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"help_text": "Type: `file`, default: `$id.$key.coverage_gtf.gtf`. "
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,
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"default":"$id.$key.coverage_gtf.gtf"
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}
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,
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"abundance": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.abundance.txt`. ",
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"help_text": "Type: `file`, default: `$id.$key.abundance.txt`. "
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,
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"default":"$id.$key.abundance.txt"
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}
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,
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"ballgown": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.ballgown.ballgown`. for running ballgown",
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"help_text": "Type: `file`, default: `$id.$key.ballgown.ballgown`. for running ballgown"
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,
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"default":"$id.$key.ballgown.ballgown"
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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"
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},
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{
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"$ref": "#/definitions/output"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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