CI
8ccd0dfd21
Build pipeline: viash-hub.biobox.seqtk-sample-plh2n
Source commit: 796c3bcdbb
Source message: changelog entry added
197 lines
7.4 KiB
JSON
197 lines
7.4 KiB
JSON
{
|
|
"$schema": "http://json-schema.org/draft-07/schema",
|
|
"title": "samtools_faidx",
|
|
"description": "Indexes FASTA files to enable random access to fasta and fastq files.",
|
|
"type": "object",
|
|
"definitions": {
|
|
|
|
|
|
|
|
"inputs" : {
|
|
"title": "Inputs",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"input": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`. FASTA input file",
|
|
"help_text": "Type: `file`. FASTA input file.\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"length": {
|
|
"type":
|
|
"integer",
|
|
"description": "Type: `integer`, default: `60`. Length for FASTA sequence line wrapping",
|
|
"help_text": "Type: `integer`, default: `60`. Length for FASTA sequence line wrapping. If zero, this means do not\nline wrap. Defaults to the line length in the input file.\n"
|
|
,
|
|
"default": "60"
|
|
}
|
|
|
|
|
|
,
|
|
"region_file": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`. File of regions",
|
|
"help_text": "Type: `file`. File of regions. Format is chr:from-to. One per line.\nMust be used with --output to avoid sending output to stdout.\n"
|
|
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"outputs" : {
|
|
"title": "Outputs",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"output": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, required, default: `$id.$key.output.fasta`, example: `output.fasta`. Write output to file",
|
|
"help_text": "Type: `file`, required, default: `$id.$key.output.fasta`, example: `output.fasta`. Write output to file.\n"
|
|
,
|
|
"default": "$id.$key.output.fasta"
|
|
}
|
|
|
|
|
|
,
|
|
"mark_strand": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, default: `rc`. Add strand indicator to sequence name",
|
|
"help_text": "Type: `string`, default: `rc`. Add strand indicator to sequence name. Options are:\n[ rc, no, sign, custom,\u003cpos\u003e,\u003cneg\u003e ]\n"
|
|
,
|
|
"default": "rc"
|
|
}
|
|
|
|
|
|
,
|
|
"fai_idx": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, default: `$id.$key.fai_idx.fai`, example: `file.fa.fai`. Read/Write to specified index file (default file",
|
|
"help_text": "Type: `file`, default: `$id.$key.fai_idx.fai`, example: `file.fa.fai`. Read/Write to specified index file (default file.fa.fai).\n"
|
|
,
|
|
"default": "$id.$key.fai_idx.fai"
|
|
}
|
|
|
|
|
|
,
|
|
"gzi_idx": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, default: `$id.$key.gzi_idx.gzi`, example: `file.fa.gz.gzi`. Read/Write to specified compressed file index (used with ",
|
|
"help_text": "Type: `file`, default: `$id.$key.gzi_idx.gzi`, example: `file.fa.gz.gzi`. Read/Write to specified compressed file index (used with .gz files, default file.fa.gz.gzi).\n"
|
|
,
|
|
"default": "$id.$key.gzi_idx.gzi"
|
|
}
|
|
|
|
|
|
,
|
|
"fastq": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Read FASTQ files and output extracted sequences in FASTQ format",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Read FASTQ files and output extracted sequences in FASTQ format. Same as using samtools fqidx.\n"
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"options" : {
|
|
"title": "Options",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"continue": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Continue working if a non-existent region is requested",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Continue working if a non-existent region is requested.\n"
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
,
|
|
"reverse_complement": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. Reverse complement sequences",
|
|
"help_text": "Type: `boolean_true`, default: `false`. Reverse complement sequences.\n"
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"nextflow input-output arguments" : {
|
|
"title": "Nextflow input-output arguments",
|
|
"type": "object",
|
|
"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.",
|
|
"properties": {
|
|
|
|
|
|
"publish_dir": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
|
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"param_list": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
|
|
"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.",
|
|
"hidden": true
|
|
|
|
}
|
|
|
|
|
|
}
|
|
}
|
|
},
|
|
"allOf": [
|
|
|
|
{
|
|
"$ref": "#/definitions/inputs"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/outputs"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/options"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|