CI
884fc9474e
Build pipeline: viash-hub.biobox.v0.2-s4bkm
Source commit: f22ab0eab5
Source message: Prep v0.2.0
116 lines
4.4 KiB
JSON
116 lines
4.4 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "samtools_idxstats",
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"description": "Reports alignment summary statistics for a BAM file.",
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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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"bam": {
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"type":
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"string",
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"description": "Type: `file`. BAM input file",
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"help_text": "Type: `file`. BAM input file."
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}
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,
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"bai": {
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"type":
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"string",
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"description": "Type: `file`. BAM index file",
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"help_text": "Type: `file`. BAM index file."
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}
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,
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"fasta": {
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"type":
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"string",
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"description": "Type: `file`. Reference file the CRAM was created with (optional)",
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"help_text": "Type: `file`. Reference file the CRAM was created with (optional)."
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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.$key.output.idxstats`, example: `output.idxstats`. File containing samtools stats output in tab-delimited format",
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"help_text": "Type: `file`, required, default: `$id.$key.output.idxstats`, example: `output.idxstats`. File containing samtools stats output in tab-delimited format.\n"
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,
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"default": "$id.$key.output.idxstats"
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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/nextflow input-output arguments"
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}
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]
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}
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