CI
50e78b4b9a
Build pipeline: viash-hub.rnaseq.v0.1-gnwkh
Source commit: fd0354dae8
Source message: Point to new assets dir
151 lines
6.2 KiB
JSON
151 lines
6.2 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "rseqc_readduplication",
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"description": "Calculate read duplication rate.\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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"read_count_upper_limit": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `500`. Upper limit of reads\u0027 occurence",
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"help_text": "Type: `integer`, default: `500`. Upper limit of reads\u0027 occurence. Only used for plotting, default = 500 (times)."
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,
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"default": "500"
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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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},
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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_duplication_rate_plot_r": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_duplication_rate_plot_r.r`. R script for generating duplication rate plot",
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"help_text": "Type: `file`, default: `$id.$key.output_duplication_rate_plot_r.r`. R script for generating duplication rate plot"
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,
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"default": "$id.$key.output_duplication_rate_plot_r.r"
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}
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,
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"output_duplication_rate_plot": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_duplication_rate_plot.pdf`. duplication rate plot (pdf)",
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"help_text": "Type: `file`, default: `$id.$key.output_duplication_rate_plot.pdf`. duplication rate plot (pdf)"
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,
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"default": "$id.$key.output_duplication_rate_plot.pdf"
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}
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,
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"output_duplication_rate_mapping": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication",
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"help_text": "Type: `file`, default: `$id.$key.output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication"
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,
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"default": "$id.$key.output_duplication_rate_mapping.xls"
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}
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,
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"output_duplication_rate_sequence": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication",
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"help_text": "Type: `file`, default: `$id.$key.output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication"
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,
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"default": "$id.$key.output_duplication_rate_sequence.xls"
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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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