CI
c00bcda3f8
Build pipeline: viash-hub.rnaseq.main-k4ttq
Source commit: f52978a0e2
Source message: Fix summarizedexperiment build (#42)
249 lines
9.0 KiB
JSON
249 lines
9.0 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "merge_quant_results",
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"description": "A sub-workflow to merge the counts obtained from salmon quant across all samples.",
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"type": "object",
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"definitions": {
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"input" : {
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"title": "Input",
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"type": "object",
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"description": "No description",
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"properties": {
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"salmon_quant_results": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"kallisto_quant_results": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"gtf": {
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"type":
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"string",
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"description": "Type: `file`. ",
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"help_text": "Type: `file`. "
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}
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,
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"gtf_extra_attributes": {
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"type":
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"string",
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"description": "Type: `string`, default: `gene_name`. ",
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"help_text": "Type: `string`, default: `gene_name`. "
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,
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"default":"gene_name"
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}
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,
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"gtf_group_features": {
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"type":
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"string",
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"description": "Type: `string`, default: `gene_id`. ",
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"help_text": "Type: `string`, default: `gene_id`. "
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,
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"default":"gene_id"
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}
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,
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"quant_type": {
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"type":
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"string",
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"description": "Type: `string`, default: `salmon`, choices: ``salmon`, `kallisto``. Quantification method used",
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"help_text": "Type: `string`, default: `salmon`, choices: ``salmon`, `kallisto``. Quantification method used.",
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"enum": ["salmon", "kallisto"]
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,
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"default":"salmon"
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}
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,
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"versions": {
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"type":
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"string",
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"description": "Type: `file`. ",
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"help_text": "Type: `file`. "
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}
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}
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},
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"output" : {
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"title": "Output",
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"type": "object",
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"description": "No description",
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"properties": {
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"tpm_gene": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.tpm_gene.tsv`, example: `gene_tpm.tsv`. ",
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"help_text": "Type: `file`, default: `$id.$key.tpm_gene.tsv`, example: `gene_tpm.tsv`. "
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,
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"default":"$id.$key.tpm_gene.tsv"
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}
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,
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"counts_gene": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.counts_gene.tsv`, example: `gene_counts.tsv`. ",
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"help_text": "Type: `file`, default: `$id.$key.counts_gene.tsv`, example: `gene_counts.tsv`. "
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,
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"default":"$id.$key.counts_gene.tsv"
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}
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,
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"counts_gene_length_scaled": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`, example: `gene_counts_length_scaled.tsv`. ",
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"help_text": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`, example: `gene_counts_length_scaled.tsv`. "
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,
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"default":"$id.$key.counts_gene_length_scaled.tsv"
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}
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,
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"counts_gene_scaled": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`, example: `gene_counts_scaled.tsv`. ",
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"help_text": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`, example: `gene_counts_scaled.tsv`. "
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,
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"default":"$id.$key.counts_gene_scaled.tsv"
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}
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,
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"tpm_transcript": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`, example: `transcript_tpm.tsv`. ",
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"help_text": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`, example: `transcript_tpm.tsv`. "
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,
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"default":"$id.$key.tpm_transcript.tsv"
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}
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,
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"lengths_gene": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.lengths_gene.tsv`, example: `gene_length.tsv`. ",
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"help_text": "Type: `file`, default: `$id.$key.lengths_gene.tsv`, example: `gene_length.tsv`. "
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,
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"default":"$id.$key.lengths_gene.tsv"
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}
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,
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"counts_transcript": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.counts_transcript.tsv`, example: `transcript_counts.tsv`. ",
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"help_text": "Type: `file`, default: `$id.$key.counts_transcript.tsv`, example: `transcript_counts.tsv`. "
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,
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"default":"$id.$key.counts_transcript.tsv"
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}
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,
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"lengths_transcript": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.lengths_transcript.tsv`, example: `transcript_length.tsv`. ",
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"help_text": "Type: `file`, default: `$id.$key.lengths_transcript.tsv`, example: `transcript_length.tsv`. "
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,
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"default":"$id.$key.lengths_transcript.tsv"
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}
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,
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"quant_merged_summarizedexperiment": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.quant_merged_summarizedexperiment`, example: `quant_merged_summarizedexperiment`. ",
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"help_text": "Type: `file`, default: `$id.$key.quant_merged_summarizedexperiment`, example: `quant_merged_summarizedexperiment`. "
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,
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"default":"$id.$key.quant_merged_summarizedexperiment"
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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/input"
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},
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{
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"$ref": "#/definitions/output"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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