CI
bb7533583f
Build pipeline: vsh-ci-dev-gckj5
Source commit: da62b4ffe3
Source message: Add labels to qc_test component
230 lines
8.0 KiB
JSON
230 lines
8.0 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "scsplit",
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"description": "scsplit is a genotype-free demultiplexing methode of pooled single-cell RNA-seq, using a hidden state model for identifying genetically distinct samples within a mixed population.",
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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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"vcf": {
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"type":
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"string",
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"description": "Type: `file`. VCF from mixed BAM",
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"help_text": "Type: `file`. VCF from mixed BAM"
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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`. mixed sample BAM",
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"help_text": "Type: `file`. mixed sample BAM"
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}
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,
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"bar": {
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"type":
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"string",
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"description": "Type: `file`. barcodes whitelist",
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"help_text": "Type: `file`. barcodes whitelist"
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}
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,
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"tag": {
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"type":
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"string",
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"description": "Type: `string`, default: `CB`. tag for barcode",
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"help_text": "Type: `string`, default: `CB`. tag for barcode"
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,
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"default": "CB"
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}
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,
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"com": {
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"type":
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"string",
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"description": "Type: `file`. common SNVs",
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"help_text": "Type: `file`. common SNVs"
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}
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,
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"num": {
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"type":
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"integer",
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"description": "Type: `integer`. expected number of mixed samples",
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"help_text": "Type: `integer`. expected number of mixed samples"
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}
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,
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"sub": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `10`. maximum number of subpopulations in autodetect mode",
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"help_text": "Type: `integer`, default: `10`. maximum number of subpopulations in autodetect mode"
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,
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"default": "10"
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}
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,
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"ems": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `30`. number of EM repeats to avoid local maximum",
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"help_text": "Type: `integer`, default: `30`. number of EM repeats to avoid local maximum"
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,
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"default": "30"
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}
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,
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"dbl": {
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"type":
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"number",
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"description": "Type: `double`. correction for doublets",
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"help_text": "Type: `double`. correction for doublets. There will be no refinement on the results if this optional parameter is not specified or specified percentage is less than doublet rates detected during the run."
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}
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,
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"vcf_known": {
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"type":
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"string",
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"description": "Type: `file`. known individual genotypes to limit distinguishing variants to available variants, so that users do not need to redo genotyping on selected variants, otherwise any variants could be selected as distinguishing variants",
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"help_text": "Type: `file`. known individual genotypes to limit distinguishing variants to available variants, so that users do not need to redo genotyping on selected variants, otherwise any variants could be selected as distinguishing variants."
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}
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,
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"geno": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. generate sample genotypes based on the split result",
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"help_text": "Type: `boolean_true`, default: `false`. generate sample genotypes based on the split result."
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,
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"default": "False"
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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": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output.output`, example: `scSplit_out`. Output directory",
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"help_text": "Type: `file`, default: `$id.$key.output.output`, example: `scSplit_out`. Output directory"
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,
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"default": "$id.$key.output.output"
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}
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,
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"ref": {
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"type":
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"string",
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"description": "Type: `string`. output Ref count matrix",
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"help_text": "Type: `string`. output Ref count matrix"
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}
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,
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"alt": {
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"type":
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"string",
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"description": "Type: `string`. output Alt count matrix",
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"help_text": "Type: `string`. output Alt count matrix"
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}
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,
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"psc": {
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"type":
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"string",
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"description": "Type: `string`. generated P(S|C)",
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"help_text": "Type: `string`. generated P(S|C)"
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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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