CI
9c30676332
Build pipeline: vsh-ci-template-p9886
Source commit: d0c648fb7e
Source message: Delete src/bgzip directory (#64)
It was moved to toolbox
197 lines
7.4 KiB
JSON
197 lines
7.4 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "samtools_faidx",
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"description": "Indexes FASTA files to enable random access to fasta and fastq files.",
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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`. FASTA input file",
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"help_text": "Type: `file`. FASTA input file.\n"
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}
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,
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"length": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `60`. Length for FASTA sequence line wrapping",
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"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"
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,
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"default": "60"
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}
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,
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"region_file": {
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"type":
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"string",
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"description": "Type: `file`. File of regions",
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"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"
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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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"output": {
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"type":
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"string",
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"description": "Type: `file`, required, default: `$id.$key.output.fasta`, example: `output.fasta`. Write output to file",
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"help_text": "Type: `file`, required, default: `$id.$key.output.fasta`, example: `output.fasta`. Write output to file.\n"
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,
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"default": "$id.$key.output.fasta"
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}
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,
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"mark_strand": {
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"type":
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"string",
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"description": "Type: `string`, default: `rc`. Add strand indicator to sequence name",
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"help_text": "Type: `string`, default: `rc`. Add strand indicator to sequence name. Options are:\n[ rc, no, sign, custom,\u003cpos\u003e,\u003cneg\u003e ]\n"
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,
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"default": "rc"
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}
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,
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"fai_idx": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.fai_idx.fai`, example: `file.fa.fai`. Read/Write to specified index file (default file",
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"help_text": "Type: `file`, default: `$id.$key.fai_idx.fai`, example: `file.fa.fai`. Read/Write to specified index file (default file.fa.fai).\n"
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,
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"default": "$id.$key.fai_idx.fai"
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}
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,
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"gzi_idx": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.gzi_idx.gzi`, example: `file.fa.gz.gzi`. Read/Write to specified compressed file index (used with ",
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"help_text": "Type: `file`, default: `$id.$key.gzi_idx.gzi`, example: `file.fa.gz.gzi`. Read/Write to specified compressed file index (used with .gz files, default file.fa.gz.gzi).\n"
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,
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"default": "$id.$key.gzi_idx.gzi"
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}
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,
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"fastq": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Read FASTQ files and output extracted sequences in FASTQ format",
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"help_text": "Type: `boolean_true`, default: `false`. Read FASTQ files and output extracted sequences in FASTQ format. Same as using samtools fqidx.\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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"options" : {
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"title": "Options",
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"type": "object",
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"description": "No description",
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"properties": {
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"continue": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Continue working if a non-existent region is requested",
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"help_text": "Type: `boolean_true`, default: `false`. Continue working if a non-existent region is requested.\n"
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,
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"default": "False"
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}
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,
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"reverse_complement": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Reverse complement sequences",
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"help_text": "Type: `boolean_true`, default: `false`. Reverse complement sequences.\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/options"
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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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