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
221 lines
8.8 KiB
JSON
221 lines
8.8 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "qualimap",
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"description": "RNA-seq QC analysis using the qualimap \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. path to input mapping file in BAM format",
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"help_text": "Type: `file`, required. path to input mapping file in BAM format."
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}
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,
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"gtf": {
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"type":
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"string",
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"description": "Type: `file`, required. path to annotations file in Ensembl GTF format",
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"help_text": "Type: `file`, required. path to annotations file in Ensembl GTF format."
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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_dir": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_dir.qualimap_output`. path to output directory for raw data and report",
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"help_text": "Type: `file`, default: `$id.$key.output_dir.qualimap_output`. path to output directory for raw data and report."
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,
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"default": "$id.$key.output_dir.qualimap_output"
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}
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,
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"output_pdf": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_pdf.pdf`. path to output file for pdf report",
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"help_text": "Type: `file`, default: `$id.$key.output_pdf.pdf`. path to output file for pdf report."
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,
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"default": "$id.$key.output_pdf.pdf"
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}
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,
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"output_format": {
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"type":
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"string",
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"description": "Type: `string`, default: `html`. Format of the output report (PDF or HTML, default is HTML)",
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"help_text": "Type: `string`, default: `html`. Format of the output report (PDF or HTML, default is HTML)"
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,
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"default": "html"
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}
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}
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},
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"optional" : {
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"title": "Optional",
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"type": "object",
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"description": "No description",
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"properties": {
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"pr_bases": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `100`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias (default = 100)",
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"help_text": "Type: `integer`, default: `100`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias (default = 100)."
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,
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"default": "100"
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}
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,
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"tr_bias": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `1000`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias (default = 1000)",
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"help_text": "Type: `integer`, default: `1000`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias (default = 1000)."
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,
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"default": "1000"
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}
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,
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"algorithm": {
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"type":
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"string",
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"description": "Type: `string`, default: `uniquely-mapped-reads`. Counting algorithm (uniquely-mapped-reads (default) or proportional)",
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"help_text": "Type: `string`, default: `uniquely-mapped-reads`. Counting algorithm (uniquely-mapped-reads (default) or proportional)."
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,
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"default": "uniquely-mapped-reads"
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}
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,
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"sequencing_protocol": {
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"type":
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"string",
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"description": "Type: `string`, default: `non-strand-specific`, choices: ``non-strand-specific`, `strand-specific-reverse`, `strand-specific-forward``. Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default))",
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"help_text": "Type: `string`, default: `non-strand-specific`, choices: ``non-strand-specific`, `strand-specific-reverse`, `strand-specific-forward``. Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default)).",
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"enum": ["non-strand-specific", "strand-specific-reverse", "strand-specific-forward"]
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,
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"default": "non-strand-specific"
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}
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,
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"paired": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads",
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"help_text": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads."
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,
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"default": "False"
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}
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,
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"sorted": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name",
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"help_text": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed. Only requiredfor paired-end analysis."
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,
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"default": "False"
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}
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,
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"java_memory_size": {
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"type":
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"string",
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"description": "Type: `string`, default: `4G`. maximum Java heap memory size, default = 4G",
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"help_text": "Type: `string`, default: `4G`. maximum Java heap memory size, default = 4G."
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,
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"default": "4G"
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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/optional"
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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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