CI
a95268a2b5
Build pipeline: viash-hub.htrnaseq.main-mjsqg
Source commit: cb58990a33
Source message: Fix create_report build after R update (#52)
146 lines
6.5 KiB
JSON
146 lines
6.5 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "generate_well_statistics",
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"description": "Generate summary statistics from BAM files generated by STAR solo.",
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"type": "object",
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"definitions": {
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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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"input": {
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"type":
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"string",
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"description": "Type: `file`, example: `input.bam`. The ",
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"help_text": "Type: `file`, example: `input.bam`. The .bam file as returned by the mapping tool STAR."
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}
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,
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"barcode": {
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"type":
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"string",
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"description": "Type: `string`, required. The barcode for the well that is being processed",
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"help_text": "Type: `string`, required. The barcode for the well that is being processed. Is only used to add a metadata\ncolumn to all output files.\n"
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}
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,
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"well_id": {
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"type":
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"string",
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"description": "Type: `string`, required. ID of this well",
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"help_text": "Type: `string`, required. ID of this well. Only used to add a metadata column to the output files.\n"
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}
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,
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"processedBAMFile": {
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"type":
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"string",
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"description": "Type: `file`, default: `processedBamFile.txt`. Path to a ",
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"help_text": "Type: `file`, default: `processedBamFile.txt`. Path to a .tsv file listing, per read in the BAM file,\nthe value for the \"CB\", \"UX\", \"GX\" and \"GN\" tag, together with the\nchromsome to which the read was mapped to.\n"
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,
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"default":"processedBamFile.txt"
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}
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,
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"nrReadsNrGenesPerChrom": {
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"type":
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"string",
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"description": "Type: `file`, default: `nrReadsNrGenesPerChrom.txt`. Path to an output file that contains a ",
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"help_text": "Type: `file`, default: `nrReadsNrGenesPerChrom.txt`. Path to an output file that contains a .tsv formatted table describing\nper chromosome the number of reads that were mapped to that chromosome (NumberOfReads\ncolumn) and the number of genes on that chromosome that had at least one\nread mapped to it (NumberOfGenes).\n"
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,
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"default":"nrReadsNrGenesPerChrom.txt"
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}
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,
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"nrReadsNrUMIsPerCB": {
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"type":
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"string",
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"description": "Type: `file`, default: `nrReadsNrUMIsPerCB.txt`. Path to an output file that contains a ",
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"help_text": "Type: `file`, default: `nrReadsNrUMIsPerCB.txt`. Path to an output file that contains a .tsv formatted table describing\nper barcode the number of UMI\u0027s (nrUMIs) and the total number of reads (NumberOfReads).\n"
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,
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"default":"nrReadsNrUMIsPerCB.txt"
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}
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,
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"umiFreqTop": {
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"type":
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"string",
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"description": "Type: `file`, default: `umiFreqTop100.txt`. Path to an output file that contains a ",
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"help_text": "Type: `file`, default: `umiFreqTop100.txt`. Path to an output file that contains a .tsv formatted table describing\nper UMI (column UB) the frequency at which they occur in the reads (column\nN). Only the top 100 UMIs are included.\n"
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,
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"default":"umiFreqTop100.txt"
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}
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,
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"threads": {
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"type":
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"integer",
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"description": "Type: `integer`, default: `1`. Number of threads to use for decompressing BAM files",
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"help_text": "Type: `integer`, default: `1`. Number of threads to use for decompressing BAM files.\n"
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,
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"default":1
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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/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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