CI
1ebb61f1e8
Build pipeline: vsh-ci-dev-jsbwk
Source commit: 1e1ffb315f
Source message: Merge pull request #17 from viash-hub/add_biobox_modules
- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub
194 lines
7.7 KiB
JSON
194 lines
7.7 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "rseqc_junctionannotation",
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"description": "Compare detected splice junctions to reference gene model.\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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"input": {
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"type":
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"string",
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"description": "Type: `file`, required. input alignment file in BAM or SAM format",
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"help_text": "Type: `file`, required. input alignment file in BAM or SAM format"
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}
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,
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"refgene": {
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"type":
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"string",
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"description": "Type: `file`, required. Reference gene model in bed format",
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"help_text": "Type: `file`, required. Reference gene model in bed format"
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}
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,
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"map_qual": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30",
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"help_text": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30."
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,
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"default": "30"
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}
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,
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"min_intron": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `50`. Minimum intron length (bp), default = 50",
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"help_text": "Type: `integer`, default: `50`. Minimum intron length (bp), default = 50."
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,
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"default": "50"
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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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"output_log": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_log.log`. output log of junction annotation script",
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"help_text": "Type: `file`, default: `$id.$key.output_log.log`. output log of junction annotation script"
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,
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"default": "$id.$key.output_log.log"
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}
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,
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"output_plot_r": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_plot_r.r`. r script to generate splice_junction and splice_events plot",
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"help_text": "Type: `file`, default: `$id.$key.output_plot_r.r`. r script to generate splice_junction and splice_events plot"
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,
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"default": "$id.$key.output_plot_r.r"
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}
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,
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"output_junction_bed": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_junction_bed.bed`. junction annotation file (bed format)",
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"help_text": "Type: `file`, default: `$id.$key.output_junction_bed.bed`. junction annotation file (bed format)"
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,
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"default": "$id.$key.output_junction_bed.bed"
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}
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,
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"output_junction_interact": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_junction_interact.bed`. interact file (bed format) of junctions",
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"help_text": "Type: `file`, default: `$id.$key.output_junction_interact.bed`. interact file (bed format) of junctions. Can be uploaded to UCSC genome browser or converted to bigInteract (using bedToBigBed program) for visualization."
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,
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"default": "$id.$key.output_junction_interact.bed"
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}
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,
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"output_junction_sheet": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_junction_sheet.xls`. junction annotation file (xls format)",
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"help_text": "Type: `file`, default: `$id.$key.output_junction_sheet.xls`. junction annotation file (xls format)"
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,
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"default": "$id.$key.output_junction_sheet.xls"
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}
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,
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"output_splice_events_plot": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_splice_events_plot.pdf`. plot of splice events (pdf)",
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"help_text": "Type: `file`, default: `$id.$key.output_splice_events_plot.pdf`. plot of splice events (pdf)"
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,
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"default": "$id.$key.output_splice_events_plot.pdf"
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}
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,
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"output_splice_junctions_plot": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_splice_junctions_plot.pdf`. plot of junctions (pdf)",
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"help_text": "Type: `file`, default: `$id.$key.output_splice_junctions_plot.pdf`. plot of junctions (pdf)"
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,
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"default": "$id.$key.output_splice_junctions_plot.pdf"
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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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