CI
56a195f1bb
Build pipeline: vsh-ci-template-bbg2t
Source commit: d97e3156fe
Source message: Rename biobase -> biobox
152 lines
6.0 KiB
JSON
152 lines
6.0 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "lofreq_indelqual",
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"description": "Insert indel qualities into BAM file (required for indel predictions).\n\nThe preferred way of inserting indel qualities should be via GATK\u0027s BQSR (\u003e=2) If that\u0027s not possible, use this subcommand.\nThe command has two modes: \u0027uniform\u0027 and \u0027dindel\u0027:\n- \u0027uniform\u0027 will assign a given value uniformly, whereas\n- \u0027dindel\u0027 will insert indel qualities based on Dindel (PMID 20980555).\nBoth will overwrite any existing values.\nDo not realign your BAM file afterwards!\n",
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"type": "object",
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"definitions": {
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"inputs" : {
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"title": "Inputs",
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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, example: `normal.bam`. Input BAM file",
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"help_text": "Type: `file`, required, example: `normal.bam`. Input BAM file.\n"
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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: `file`, example: `reference.fasta`. Reference sequence used for mapping (Only required for --dindel)",
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"help_text": "Type: `file`, example: `reference.fasta`. Reference sequence used for mapping (Only required for --dindel).\n"
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}
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}
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},
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"outputs" : {
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"title": "Outputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"out": {
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"type":
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"string",
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"description": "Type: `file`, required, default: `$id.$key.out.bam`, example: `output.bam`. Output BAM file",
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"help_text": "Type: `file`, required, default: `$id.$key.out.bam`, example: `output.bam`. Output BAM file.\n"
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,
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"default": "$id.$key.out.bam"
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}
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}
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},
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"arguments" : {
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"title": "Arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"uniform": {
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"type":
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"string",
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"description": "Type: `string`, example: `50,50`. Add this indel quality uniformly to all bases",
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"help_text": "Type: `string`, example: `50,50`. Add this indel quality uniformly to all bases. Use two comma separated values to specify insertion and deletion quality separately. (clashes with --dindel).\n"
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}
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,
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"dindel": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Add Dindel\u0027s indel qualities (Illumina specific) (clashes with -u; needs --ref)",
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"help_text": "Type: `boolean_true`, default: `false`. Add Dindel\u0027s indel qualities (Illumina specific) (clashes with -u; needs --ref).\n"
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,
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"default": "False"
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}
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,
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"verbose": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Be verbose",
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"help_text": "Type: `boolean_true`, default: `false`. Be verbose.\n"
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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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"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/inputs"
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},
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{
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"$ref": "#/definitions/outputs"
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},
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{
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"$ref": "#/definitions/arguments"
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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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