CI
bb7533583f
Build pipeline: vsh-ci-dev-gckj5
Source commit: da62b4ffe3
Source message: Add labels to qc_test component
138 lines
6.4 KiB
JSON
138 lines
6.4 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "leiden",
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"description": "Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy framework] [Wolf18]. \nLeiden is an improved version of the [Louvain algorithm] [Blondel08]. \nIt has been proposed for single-cell analysis by [Levine15] [Levine15]. \nThis requires having ran `neighbors/find_neighbors` or `neighbors/bbknn` first.\n\n[Blondel08]: Blondel et al. (2008), Fast unfolding of communities in large networks, J. Stat. Mech. \n[Levine15]: Levine et al. (2015), Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis, Cell. \n[Traag18]: Traag et al. (2018), From Louvain to Leiden: guaranteeing well-connected communities arXiv. \n[Wolf18]: Wolf et al. (2018), Scanpy: large-scale single-cell gene expression data analysis, Genome Biology. \n",
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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`, required, example: `input.h5mu`. Input file",
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"help_text": "Type: `file`, required, example: `input.h5mu`. Input file."
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}
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,
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"modality": {
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"type":
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"string",
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"description": "Type: `string`, default: `rna`. ",
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"help_text": "Type: `string`, default: `rna`. "
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,
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"default": "rna"
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}
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,
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"obsp_connectivities": {
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"type":
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"string",
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"description": "Type: `string`, default: `connectivities`. In which ",
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"help_text": "Type: `string`, default: `connectivities`. In which .obsp slot the neighbor connectivities can be found."
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,
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"default": "connectivities"
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}
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,
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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.$key.output.h5mu`, example: `output.h5mu`. Output file",
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"help_text": "Type: `file`, required, default: `$id.$key.output.h5mu`, example: `output.h5mu`. Output file."
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,
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"default": "$id.$key.output.h5mu"
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}
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,
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"output_compression": {
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"type":
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"string",
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"description": "Type: `string`, example: `gzip`, choices: ``gzip`, `lzf``. ",
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"help_text": "Type: `string`, example: `gzip`, choices: ``gzip`, `lzf``. ",
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"enum": ["gzip", "lzf"]
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}
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,
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"obsm_name": {
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"type":
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"string",
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"description": "Type: `string`, default: `leiden`. Name of the ",
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"help_text": "Type: `string`, default: `leiden`. Name of the .obsm key under which to add the cluster labels.\nThe name of the columns in the matrix will correspond to the resolutions.\n"
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,
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"default": "leiden"
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}
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,
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"resolution": {
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"type":
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"string",
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"description": "Type: List of `double`, required, default: `1.0`, multiple_sep: `\";\"`. A parameter value controlling the coarseness of the clustering",
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"help_text": "Type: List of `double`, required, default: `1.0`, multiple_sep: `\";\"`. A parameter value controlling the coarseness of the clustering. Higher values lead to more clusters.\nMultiple values will result in clustering being performed multiple times.\n"
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,
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"default": "1.0"
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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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