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
160 lines
6.3 KiB
JSON
160 lines
6.3 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "rseqc_tin",
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"description": "Calculte TIN (transcript integrity number) from RNA-seq reads\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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"bam_input": {
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"type":
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"string",
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"description": "Type: `file`, required. Path to input alignment file in BAM or SAM format",
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"help_text": "Type: `file`, required. Path to input alignment file in BAM or SAM format."
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}
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,
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"bai_input": {
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"type":
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"string",
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"description": "Type: `file`, required. Path to bam index file in bai format",
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"help_text": "Type: `file`, required. Path to bam index file in bai 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. BED file containing the reference gene model",
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"help_text": "Type: `file`, required. BED file containing the reference gene model"
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}
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,
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"minimum_coverage": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `10`. Minimum number of reads mapped to a transcript, default = 10",
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"help_text": "Type: `integer`, default: `10`. Minimum number of reads mapped to a transcript, default = 10."
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,
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"default": "10"
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}
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,
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"sample_size": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `100`. Number of equal-spaced nucleotide positions picked from mRNA",
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"help_text": "Type: `integer`, default: `100`. Number of equal-spaced nucleotide positions picked from mRNA. Note, if this number is larger than the length of mRNA (L), it will be halved until it\u0027s smaller than L (default = 100)"
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,
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"default": "100"
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}
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,
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"subtract_background": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Set flag to subtract background noise (estimated from intronic reads)",
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"help_text": "Type: `boolean_true`, default: `false`. Set flag to subtract background noise (estimated from intronic reads). Only use this option if there are substantial intronic reads."
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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_tin_summary": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_tin_summary.txt`. summary statistics (txt) of calculated TIN metrics",
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"help_text": "Type: `file`, default: `$id.$key.output_tin_summary.txt`. summary statistics (txt) of calculated TIN metrics"
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,
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"default": "$id.$key.output_tin_summary.txt"
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}
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,
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"output_tin": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_tin.xls`. file with TIN metrics (xls)",
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"help_text": "Type: `file`, default: `$id.$key.output_tin.xls`. file with TIN metrics (xls)"
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,
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"default": "$id.$key.output_tin.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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