Build branch 0.1.0 with version 0.1.0 (3947a02)
Build pipeline: openpipelines-bio.openpipeline-spatial.0.1.0-8j6mj
Source commit: 3947a0286c
Source message: point to op VH release
This commit is contained in:
@@ -13,9 +13,9 @@ links:
|
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repositories:
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- name: openpipeline
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repo: openpipelines-bio/openpipeline
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type: github
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tag: 2.1.2
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repo: openpipeline
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type: vsh
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||||
tag: v3.0.0
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||||
|
||||
info:
|
||||
test_resources:
|
||||
|
||||
@@ -1,21 +0,0 @@
|
||||
# Inputs
|
||||
input: # please fill in - example: "sample_path"
|
||||
# input_column: "foo"
|
||||
# input_layer: "foo"
|
||||
modality: # please fill in - example: "rna"
|
||||
# matrix: "var"
|
||||
|
||||
# Outputs
|
||||
# output: "$id.$key.output.h5mu"
|
||||
# output_compression: "gzip"
|
||||
output_match_column: # please fill in - example: "foo"
|
||||
# output_fraction_column: "foo"
|
||||
|
||||
# Query options
|
||||
regex_pattern: # please fill in - example: "^[mM][tT]-"
|
||||
|
||||
# Nextflow input-output arguments
|
||||
publish_dir: # please fill in - example: "output/"
|
||||
# param_list: "my_params.yaml"
|
||||
|
||||
# Arguments
|
||||
@@ -1,200 +0,0 @@
|
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{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "grep_annotation_column",
|
||||
"description": "Perform a regex lookup on a column from the annotation matrices .obs or .var.\nThe annotation matrix can originate from either a modality, or all modalities (global .var or .obs).\n",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
"Dataset input": {
|
||||
"title": "Dataset input",
|
||||
"type": "object",
|
||||
"description": "Dataset input using nf-tower \"dataset\" or \"data explorer\". Allows for the input of multiple parameter sets to initialise a Nextflow channel.",
|
||||
"properties": {
|
||||
"param_list": {
|
||||
"description": "Dataset input can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob. The names of the input fields (e.g. csv columns, json keys) need to be an exact match with the workflow input parameters.",
|
||||
"default": "",
|
||||
"format": "file-path",
|
||||
"mimetype": "text/csv",
|
||||
"pattern": "^\\S+\\.csv$"
|
||||
}
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
|
||||
"inputs" : {
|
||||
"title": "Inputs",
|
||||
"type": "object",
|
||||
"description": "Arguments related to the input dataset.",
|
||||
"properties": {
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||||
|
||||
|
||||
"input": {
|
||||
"type":
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||||
"string",
|
||||
"description": "Type: `file`, required, example: `sample_path`. Path to the input ",
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"help_text": "Type: `file`, required, example: `sample_path`. Path to the input .h5mu."
|
||||
|
||||
}
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||||
|
||||
|
||||
,
|
||||
"input_column": {
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||||
"type":
|
||||
"string",
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||||
"description": "Type: `string`. Column to query",
|
||||
"help_text": "Type: `string`. Column to query. If not specified, use .var_names or .obs_names, depending on the value of --matrix"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"input_layer": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`. Input data to use when calculating fraction of observations that match with the query",
|
||||
"help_text": "Type: `string`. Input data to use when calculating fraction of observations that match with the query. \nOnly used when --output_fraction_column is provided. If not specified, .X is used.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"modality": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required, example: `rna`. Which modality to get the annotation matrix from",
|
||||
"help_text": "Type: `string`, required, example: `rna`. Which modality to get the annotation matrix from.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"matrix": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `var`, choices: ``var`, `obs``. Matrix to fetch the column from that will be searched",
|
||||
"help_text": "Type: `string`, example: `var`, choices: ``var`, `obs``. Matrix to fetch the column from that will be searched.",
|
||||
"enum": ["var", "obs"]
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||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"outputs" : {
|
||||
"title": "Outputs",
|
||||
"type": "object",
|
||||
"description": "Arguments related to how the output will be written.",
|
||||
"properties": {
|
||||
|
||||
|
||||
"output": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, default: `$id.$key.output.h5mu`, example: `output.h5mu`. ",
|
||||
"help_text": "Type: `file`, default: `$id.$key.output.h5mu`, example: `output.h5mu`. "
|
||||
,
|
||||
"default":"$id.$key.output.h5mu"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_compression": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `gzip`, choices: ``gzip`, `lzf``. The compression format to be used on the output h5mu object",
|
||||
"help_text": "Type: `string`, example: `gzip`, choices: ``gzip`, `lzf``. The compression format to be used on the output h5mu object.",
|
||||
"enum": ["gzip", "lzf"]
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_match_column": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required. Name of the column to write the result to",
|
||||
"help_text": "Type: `string`, required. Name of the column to write the result to."
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_fraction_column": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`. For the opposite axis, name of the column to write the fraction of \nobservations that matches to the pattern",
|
||||
"help_text": "Type: `string`. For the opposite axis, name of the column to write the fraction of \nobservations that matches to the pattern.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"query options" : {
|
||||
"title": "Query options",
|
||||
"type": "object",
|
||||
"description": "Options related to the query",
|
||||
"properties": {
|
||||
|
||||
|
||||
"regex_pattern": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required, example: `^[mM][tT]-`. Regex to use to match with the input column",
|
||||
"help_text": "Type: `string`, required, example: `^[mM][tT]-`. Regex to use to match with the input column."
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"nextflow input-output arguments" : {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"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.",
|
||||
"properties": {
|
||||
|
||||
|
||||
"publish_dir": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
||||
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/inputs"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/outputs"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/query options"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -1,27 +0,0 @@
|
||||
# Inputs
|
||||
input: # please fill in - example: "input.h5mu"
|
||||
modality: "rna"
|
||||
# layer: "raw_counts"
|
||||
|
||||
# Metrics added to .obs
|
||||
# var_qc_metrics: ["ercc,highly_variable,mitochondrial"]
|
||||
# var_qc_metrics_fill_na_value: true
|
||||
# top_n_vars: [123]
|
||||
output_obs_num_nonzero_vars: "num_nonzero_vars"
|
||||
output_obs_total_counts_vars: "total_counts"
|
||||
|
||||
# Metrics added to .var
|
||||
output_var_num_nonzero_obs: "num_nonzero_obs"
|
||||
output_var_total_counts_obs: "total_counts"
|
||||
output_var_obs_mean: "obs_mean"
|
||||
output_var_pct_dropout: "pct_dropout"
|
||||
|
||||
# Outputs
|
||||
# output: "$id.$key.output.h5mu"
|
||||
# output_compression: "gzip"
|
||||
|
||||
# Nextflow input-output arguments
|
||||
publish_dir: # please fill in - example: "output/"
|
||||
# param_list: "my_params.yaml"
|
||||
|
||||
# Arguments
|
||||
@@ -1,259 +0,0 @@
|
||||
{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "calculate_qc_metrics",
|
||||
"description": "Add basic quality control metrics to an .h5mu file.\n\nThe metrics are comparable to what scanpy.pp.calculate_qc_metrics output,\nalthough they have slightly different names:\n\nVar metrics (name in this component -\u003e name in scanpy):\n - pct_dropout -\u003e pct_dropout_by_{expr_type}\n - num_nonzero_obs -\u003e n_cells_by_{expr_type}\n - obs_mean -\u003e mean_{expr_type}\n - total_counts -\u003e total_{expr_type}\n\n Obs metrics:\n - num_nonzero_vars -\u003e n_genes_by_{expr_type}\n - pct_{var_qc_metrics} -\u003e pct_{expr_type}_{qc_var}\n - total_counts_{var_qc_metrics} -\u003e total_{expr_type}_{qc_var}\n - pct_of_counts_in_top_{top_n_vars}_vars -\u003e pct_{expr_type}_in_top_{n}_{var_type}\n - total_counts -\u003e total_{expr_type}\n \n",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
"Dataset input": {
|
||||
"title": "Dataset input",
|
||||
"type": "object",
|
||||
"description": "Dataset input using nf-tower \"dataset\" or \"data explorer\". Allows for the input of multiple parameter sets to initialise a Nextflow channel.",
|
||||
"properties": {
|
||||
"param_list": {
|
||||
"description": "Dataset input can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob. The names of the input fields (e.g. csv columns, json keys) need to be an exact match with the workflow input parameters.",
|
||||
"default": "",
|
||||
"format": "file-path",
|
||||
"mimetype": "text/csv",
|
||||
"pattern": "^\\S+\\.csv$"
|
||||
}
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
|
||||
"inputs" : {
|
||||
"title": "Inputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"input": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, example: `input.h5mu`. Input h5mu file",
|
||||
"help_text": "Type: `file`, required, example: `input.h5mu`. Input h5mu file"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"modality": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `rna`. ",
|
||||
"help_text": "Type: `string`, default: `rna`. "
|
||||
,
|
||||
"default":"rna"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"layer": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `raw_counts`. ",
|
||||
"help_text": "Type: `string`, example: `raw_counts`. "
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"outputs" : {
|
||||
"title": "Outputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"output": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, default: `$id.$key.output.h5mu`, example: `output.h5mu`. Output h5mu file",
|
||||
"help_text": "Type: `file`, default: `$id.$key.output.h5mu`, example: `output.h5mu`. Output h5mu file."
|
||||
,
|
||||
"default":"$id.$key.output.h5mu"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_compression": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `gzip`, choices: ``gzip`, `lzf``. The compression format to be used on the output h5mu object",
|
||||
"help_text": "Type: `string`, example: `gzip`, choices: ``gzip`, `lzf``. The compression format to be used on the output h5mu object.",
|
||||
"enum": ["gzip", "lzf"]
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"metrics added to .obs" : {
|
||||
"title": "Metrics added to .obs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"var_qc_metrics": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: List of `string`, example: `ercc,highly_variable,mitochondrial`, multiple_sep: `\";\"`. Keys to select a boolean (containing only True or False) column from ",
|
||||
"help_text": "Type: List of `string`, example: `ercc,highly_variable,mitochondrial`, multiple_sep: `\";\"`. Keys to select a boolean (containing only True or False) column from .var.\nFor each cell, calculate the proportion of total values for genes which are labeled \u0027True\u0027, \ncompared to the total sum of the values for all genes.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"var_qc_metrics_fill_na_value": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean`. Fill any \u0027NA\u0027 values found in the columns specified with --var_qc_metrics to \u0027True\u0027 or \u0027False\u0027",
|
||||
"help_text": "Type: `boolean`. Fill any \u0027NA\u0027 values found in the columns specified with --var_qc_metrics to \u0027True\u0027 or \u0027False\u0027.\nas False.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"top_n_vars": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: List of `integer`, multiple_sep: `\";\"`. Number of top vars to be used to calculate cumulative proportions",
|
||||
"help_text": "Type: List of `integer`, multiple_sep: `\";\"`. Number of top vars to be used to calculate cumulative proportions.\nIf not specified, proportions are not calculated. `--top_n_vars 20;50` finds\ncumulative proportion to the 20th and 50th most expressed vars.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_obs_num_nonzero_vars": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `num_nonzero_vars`. Name of column in ",
|
||||
"help_text": "Type: `string`, default: `num_nonzero_vars`. Name of column in .obs describing, for each observation, the number of stored values\n(including explicit zeroes). In other words, the name of the column that counts\nfor each row the number of columns that contain data.\n"
|
||||
,
|
||||
"default":"num_nonzero_vars"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_obs_total_counts_vars": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `total_counts`. Name of the column for ",
|
||||
"help_text": "Type: `string`, default: `total_counts`. Name of the column for .obs describing, for each observation (row),\nthe sum of the stored values in the columns.\n"
|
||||
,
|
||||
"default":"total_counts"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"metrics added to .var" : {
|
||||
"title": "Metrics added to .var",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"output_var_num_nonzero_obs": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `num_nonzero_obs`. Name of column describing, for each feature, the number of stored values\n(including explicit zeroes)",
|
||||
"help_text": "Type: `string`, default: `num_nonzero_obs`. Name of column describing, for each feature, the number of stored values\n(including explicit zeroes). In other words, the name of the column that counts\nfor each column the number of rows that contain data.\n"
|
||||
,
|
||||
"default":"num_nonzero_obs"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_var_total_counts_obs": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `total_counts`. Name of the column in ",
|
||||
"help_text": "Type: `string`, default: `total_counts`. Name of the column in .var describing, for each feature (column),\nthe sum of the stored values in the rows.\n"
|
||||
,
|
||||
"default":"total_counts"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_var_obs_mean": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `obs_mean`. Name of the column in ",
|
||||
"help_text": "Type: `string`, default: `obs_mean`. Name of the column in .obs providing the mean of the values in each row.\n"
|
||||
,
|
||||
"default":"obs_mean"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_var_pct_dropout": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `pct_dropout`. Name of the column in ",
|
||||
"help_text": "Type: `string`, default: `pct_dropout`. Name of the column in .obs providing for each feature the percentage of\nobservations the feature does not appear on (i.e. is missing). Same as `--num_nonzero_obs`\nbut percentage based.\n"
|
||||
,
|
||||
"default":"pct_dropout"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"nextflow input-output arguments" : {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"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.",
|
||||
"properties": {
|
||||
|
||||
|
||||
"publish_dir": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
||||
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/inputs"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/outputs"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/metrics added to .obs"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/metrics added to .var"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -1,33 +0,0 @@
|
||||
# Inputs
|
||||
id: # please fill in - example: "foo"
|
||||
input: # please fill in - example: "input.h5mu"
|
||||
modality: "rna"
|
||||
# layer: "raw_counts"
|
||||
|
||||
# Mitochondrial & Ribosomal Gene Detection
|
||||
# var_gene_names: "gene_symbol"
|
||||
# var_name_mitochondrial_genes: "foo"
|
||||
# obs_name_mitochondrial_fraction: "foo"
|
||||
mitochondrial_gene_regex: "^[mM][tT]-"
|
||||
# var_name_ribosomal_genes: "foo"
|
||||
# obs_name_ribosomal_fraction: "foo"
|
||||
ribosomal_gene_regex: "^[Mm]?[Rr][Pp][LlSs]"
|
||||
|
||||
# QC metrics calculation options
|
||||
# var_qc_metrics: ["ercc,highly_variable"]
|
||||
top_n_vars: [50, 100, 200, 500]
|
||||
output_obs_num_nonzero_vars: "num_nonzero_vars"
|
||||
output_obs_total_counts_vars: "total_counts"
|
||||
output_var_num_nonzero_obs: "num_nonzero_obs"
|
||||
output_var_total_counts_obs: "total_counts"
|
||||
output_var_obs_mean: "obs_mean"
|
||||
output_var_pct_dropout: "pct_dropout"
|
||||
|
||||
# Outputs
|
||||
# output: "$id.$key.output.h5mu"
|
||||
|
||||
# Nextflow input-output arguments
|
||||
publish_dir: # please fill in - example: "output/"
|
||||
# param_list: "my_params.yaml"
|
||||
|
||||
# Arguments
|
||||
@@ -1,320 +0,0 @@
|
||||
{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "qc",
|
||||
"description": "A pipeline to add basic qc statistics to a MuData ",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
"Dataset input": {
|
||||
"title": "Dataset input",
|
||||
"type": "object",
|
||||
"description": "Dataset input using nf-tower \"dataset\" or \"data explorer\". Allows for the input of multiple parameter sets to initialise a Nextflow channel.",
|
||||
"properties": {
|
||||
"param_list": {
|
||||
"description": "Dataset input can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob. The names of the input fields (e.g. csv columns, json keys) need to be an exact match with the workflow input parameters.",
|
||||
"default": "",
|
||||
"format": "file-path",
|
||||
"mimetype": "text/csv",
|
||||
"pattern": "^\\S+\\.csv$"
|
||||
}
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
|
||||
"inputs" : {
|
||||
"title": "Inputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"id": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required, example: `foo`. ID of the sample",
|
||||
"help_text": "Type: `string`, required, example: `foo`. ID of the sample."
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"input": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, example: `input.h5mu`. Path to the sample",
|
||||
"help_text": "Type: `file`, required, example: `input.h5mu`. Path to the sample."
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"modality": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `rna`. Which modality to process",
|
||||
"help_text": "Type: `string`, default: `rna`. Which modality to process."
|
||||
,
|
||||
"default":"rna"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"layer": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `raw_counts`. Layer to calculate qc metrics for",
|
||||
"help_text": "Type: `string`, example: `raw_counts`. Layer to calculate qc metrics for."
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"outputs" : {
|
||||
"title": "Outputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"output": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, default: `$id.$key.output.h5mu`, example: `output.h5mu`. Destination path to the output",
|
||||
"help_text": "Type: `file`, required, default: `$id.$key.output.h5mu`, example: `output.h5mu`. Destination path to the output."
|
||||
,
|
||||
"default":"$id.$key.output.h5mu"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"mitochondrial & ribosomal gene detection" : {
|
||||
"title": "Mitochondrial & Ribosomal Gene Detection",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"var_gene_names": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `gene_symbol`. ",
|
||||
"help_text": "Type: `string`, example: `gene_symbol`. .var column name to be used to detect mitochondrial/ribosomal genes instead of .var_names (default if not set).\nGene names matching with the regex value from --mitochondrial_gene_regex or --ribosomal_gene_regex will be \nidentified as mitochondrial or ribosomal genes, respectively.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"var_name_mitochondrial_genes": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`. In which ",
|
||||
"help_text": "Type: `string`. In which .var slot to store a boolean array corresponding the mitochondrial genes.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"obs_name_mitochondrial_fraction": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`. ",
|
||||
"help_text": "Type: `string`. .Obs slot to store the fraction of reads found to be mitochondrial. Defaults to \u0027fraction_\u0027 suffixed by the value of --var_name_mitochondrial_genes\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"mitochondrial_gene_regex": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `^[mM][tT]-`. Regex string that identifies mitochondrial genes from --var_gene_names",
|
||||
"help_text": "Type: `string`, default: `^[mM][tT]-`. Regex string that identifies mitochondrial genes from --var_gene_names.\nBy default will detect human and mouse mitochondrial genes from a gene symbol.\n"
|
||||
,
|
||||
"default":"^[mM][tT]-"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"var_name_ribosomal_genes": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`. In which ",
|
||||
"help_text": "Type: `string`. In which .var slot to store a boolean array corresponding the ribosomal genes.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"obs_name_ribosomal_fraction": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`. When specified, write the fraction of counts originating from ribosomal genes \n(based on --ribosomal_gene_regex) to an ",
|
||||
"help_text": "Type: `string`. When specified, write the fraction of counts originating from ribosomal genes \n(based on --ribosomal_gene_regex) to an .obs column with the specified name.\nRequires --var_name_ribosomal_genes.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"ribosomal_gene_regex": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `^[Mm]?[Rr][Pp][LlSs]`. Regex string that identifies ribosomal genes from --var_gene_names",
|
||||
"help_text": "Type: `string`, default: `^[Mm]?[Rr][Pp][LlSs]`. Regex string that identifies ribosomal genes from --var_gene_names.\nBy default will detect human and mouse ribosomal genes from a gene symbol.\n"
|
||||
,
|
||||
"default":"^[Mm]?[Rr][Pp][LlSs]"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"qc metrics calculation options" : {
|
||||
"title": "QC metrics calculation options",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"var_qc_metrics": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: List of `string`, example: `ercc,highly_variable`, multiple_sep: `\",\"`. Keys to select a boolean (containing only True or False) column from ",
|
||||
"help_text": "Type: List of `string`, example: `ercc,highly_variable`, multiple_sep: `\",\"`. Keys to select a boolean (containing only True or False) column from .var.\nFor each cell, calculate the proportion of total values for genes which are labeled \u0027True\u0027, \ncompared to the total sum of the values for all genes. Defaults to the value from\n--var_name_mitochondrial_genes.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"top_n_vars": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: List of `integer`, default: `50,100,200,500`, multiple_sep: `\",\"`. Number of top vars to be used to calculate cumulative proportions",
|
||||
"help_text": "Type: List of `integer`, default: `50,100,200,500`, multiple_sep: `\",\"`. Number of top vars to be used to calculate cumulative proportions.\nIf not specified, proportions are not calculated. `--top_n_vars 20,50` finds\ncumulative proportion to the 20th and 50th most expressed vars.\n"
|
||||
,
|
||||
"default":"50,100,200,500"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_obs_num_nonzero_vars": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `num_nonzero_vars`. Name of column in ",
|
||||
"help_text": "Type: `string`, default: `num_nonzero_vars`. Name of column in .obs describing, for each observation, the number of stored values\n(including explicit zeroes). In other words, the name of the column that counts\nfor each row the number of columns that contain data.\n"
|
||||
,
|
||||
"default":"num_nonzero_vars"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_obs_total_counts_vars": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `total_counts`. Name of the column for ",
|
||||
"help_text": "Type: `string`, default: `total_counts`. Name of the column for .obs describing, for each observation (row),\nthe sum of the stored values in the columns.\n"
|
||||
,
|
||||
"default":"total_counts"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_var_num_nonzero_obs": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `num_nonzero_obs`. Name of column describing, for each feature, the number of stored values\n(including explicit zeroes)",
|
||||
"help_text": "Type: `string`, default: `num_nonzero_obs`. Name of column describing, for each feature, the number of stored values\n(including explicit zeroes). In other words, the name of the column that counts\nfor each column the number of rows that contain data.\n"
|
||||
,
|
||||
"default":"num_nonzero_obs"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_var_total_counts_obs": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `total_counts`. Name of the column in ",
|
||||
"help_text": "Type: `string`, default: `total_counts`. Name of the column in .var describing, for each feature (column),\nthe sum of the stored values in the rows.\n"
|
||||
,
|
||||
"default":"total_counts"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_var_obs_mean": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `obs_mean`. Name of the column in ",
|
||||
"help_text": "Type: `string`, default: `obs_mean`. Name of the column in .obs providing the mean of the values in each row.\n"
|
||||
,
|
||||
"default":"obs_mean"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"output_var_pct_dropout": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, default: `pct_dropout`. Name of the column in ",
|
||||
"help_text": "Type: `string`, default: `pct_dropout`. Name of the column in .obs providing for each feature the percentage of\nobservations the feature does not appear on (i.e. is missing). Same as `--output_var_num_nonzero_obs`\nbut percentage based.\n"
|
||||
,
|
||||
"default":"pct_dropout"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"nextflow input-output arguments" : {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"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.",
|
||||
"properties": {
|
||||
|
||||
|
||||
"publish_dir": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
||||
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/inputs"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/outputs"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/mitochondrial & ribosomal gene detection"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/qc metrics calculation options"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "grep_annotation_column"
|
||||
namespace: "metadata"
|
||||
version: "2.1.2"
|
||||
version: "v3.0.0"
|
||||
authors:
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
@@ -83,6 +83,7 @@ argument_groups:
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Location of the output MuData file.\n"
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
@@ -92,19 +93,6 @@ argument_groups:
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
description: "The compression format to be used on the output h5mu object."
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_match_column"
|
||||
description: "Name of the column to write the result to."
|
||||
@@ -122,6 +110,20 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
description: "Compression format to use for the output AnnData and/or Mudata objects.\n\
|
||||
By default no compression is applied.\n"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Query options"
|
||||
description: "Options related to the query"
|
||||
arguments:
|
||||
@@ -238,7 +240,8 @@ engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.11-slim"
|
||||
target_tag: "2.1.0"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v3.0.0"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
@@ -268,18 +271,21 @@ engines:
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/metadata/grep_annotation_column/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "docker"
|
||||
engine: "docker|native"
|
||||
output: "target/nextflow/metadata/grep_annotation_column"
|
||||
executable: "target/nextflow/metadata/grep_annotation_column/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "a0c9522486585774f76416150f8a3291409b5363"
|
||||
git_commit: "e92e56b49125af8ef2ebb11586191a6cbf9a8457"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "2.1.1-2-ga0c95224865"
|
||||
git_tag: "0.2.0-2059-ge92e56b4"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "v3.0.0"
|
||||
summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
|
||||
description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
|
||||
\ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
|
||||
@@ -296,6 +302,10 @@ package_config:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
nextflow_labels_ci:
|
||||
- path: "src/workflows/utils/labels_ci.config"
|
||||
description: "Adds the correct memory and CPU labels when running on the Viash\
|
||||
\ Hub CI."
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
@@ -303,13 +313,14 @@ package_config:
|
||||
- ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
|
||||
)'"
|
||||
- ".version := \"2.1.2\""
|
||||
- ".engines[.type == 'docker'].target_tag := '2.1.0'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v3.0.0'"
|
||||
keywords:
|
||||
- "single-cell"
|
||||
- "multimodal"
|
||||
license: "MIT"
|
||||
organization: "openpipelines-bio"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -1,4 +1,4 @@
|
||||
// grep_annotation_column 2.1.2
|
||||
// grep_annotation_column v3.0.0
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -3035,7 +3035,7 @@ meta = [
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "grep_annotation_column",
|
||||
"namespace" : "metadata",
|
||||
"version" : "2.1.2",
|
||||
"version" : "v3.0.0",
|
||||
"authors" : [
|
||||
{
|
||||
"name" : "Dries Schaumont",
|
||||
@@ -3140,6 +3140,7 @@ meta = [
|
||||
"alternatives" : [
|
||||
"-o"
|
||||
],
|
||||
"description" : "Location of the output MuData file.\n",
|
||||
"example" : [
|
||||
"output.h5mu"
|
||||
],
|
||||
@@ -3150,22 +3151,6 @@ meta = [
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "string",
|
||||
"name" : "--output_compression",
|
||||
"description" : "The compression format to be used on the output h5mu object.",
|
||||
"example" : [
|
||||
"gzip"
|
||||
],
|
||||
"required" : false,
|
||||
"choices" : [
|
||||
"gzip",
|
||||
"lzf"
|
||||
],
|
||||
"direction" : "input",
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "string",
|
||||
"name" : "--output_match_column",
|
||||
@@ -3183,6 +3168,22 @@ meta = [
|
||||
"direction" : "input",
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "string",
|
||||
"name" : "--output_compression",
|
||||
"description" : "Compression format to use for the output AnnData and/or Mudata objects.\nBy default no compression is applied.\n",
|
||||
"example" : [
|
||||
"gzip"
|
||||
],
|
||||
"required" : false,
|
||||
"choices" : [
|
||||
"gzip",
|
||||
"lzf"
|
||||
],
|
||||
"direction" : "input",
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
}
|
||||
]
|
||||
},
|
||||
@@ -3333,7 +3334,8 @@ meta = [
|
||||
"type" : "docker",
|
||||
"id" : "docker",
|
||||
"image" : "python:3.11-slim",
|
||||
"target_tag" : "2.1.0",
|
||||
"target_registry" : "images.viash-hub.com",
|
||||
"target_tag" : "v3.0.0",
|
||||
"namespace_separator" : "/",
|
||||
"setup" : [
|
||||
{
|
||||
@@ -3376,20 +3378,25 @@ meta = [
|
||||
"upgrade" : true
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"type" : "native",
|
||||
"id" : "native"
|
||||
}
|
||||
],
|
||||
"build_info" : {
|
||||
"config" : "/home/runner/work/openpipeline/openpipeline/src/metadata/grep_annotation_column/config.vsh.yaml",
|
||||
"config" : "/workdir/root/repo/src/metadata/grep_annotation_column/config.vsh.yaml",
|
||||
"runner" : "nextflow",
|
||||
"engine" : "docker",
|
||||
"output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/grep_annotation_column",
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/metadata/grep_annotation_column",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "a0c9522486585774f76416150f8a3291409b5363",
|
||||
"git_commit" : "e92e56b49125af8ef2ebb11586191a6cbf9a8457",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline",
|
||||
"git_tag" : "2.1.1-2-ga0c95224865"
|
||||
"git_tag" : "0.2.0-2059-ge92e56b4"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "openpipeline",
|
||||
"version" : "v3.0.0",
|
||||
"summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
|
||||
"description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n",
|
||||
"info" : {
|
||||
@@ -3399,22 +3406,29 @@ meta = [
|
||||
"path" : "s3://openpipelines-data",
|
||||
"dest" : "resources_test"
|
||||
}
|
||||
],
|
||||
"nextflow_labels_ci" : [
|
||||
{
|
||||
"path" : "src/workflows/utils/labels_ci.config",
|
||||
"description" : "Adds the correct memory and CPU labels when running on the Viash Hub CI."
|
||||
}
|
||||
]
|
||||
},
|
||||
"viash_version" : "0.9.4",
|
||||
"source" : "/home/runner/work/openpipeline/openpipeline/src",
|
||||
"target" : "/home/runner/work/openpipeline/openpipeline/target",
|
||||
"source" : "/workdir/root/repo/src",
|
||||
"target" : "/workdir/root/repo/target",
|
||||
"config_mods" : [
|
||||
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
|
||||
".version := \\"2.1.2\\"",
|
||||
".engines[.type == 'docker'].target_tag := '2.1.0'"
|
||||
".engines += { type: \\"native\\" }",
|
||||
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
|
||||
".engines[.type == 'docker'].target_tag := 'v3.0.0'"
|
||||
],
|
||||
"keywords" : [
|
||||
"single-cell",
|
||||
"multimodal"
|
||||
],
|
||||
"license" : "MIT",
|
||||
"organization" : "openpipelines-bio",
|
||||
"organization" : "vsh",
|
||||
"links" : {
|
||||
"repository" : "https://github.com/openpipelines-bio/openpipeline",
|
||||
"docker_registry" : "ghcr.io",
|
||||
@@ -3454,9 +3468,9 @@ par = {
|
||||
'modality': $( if [ ! -z ${VIASH_PAR_MODALITY+x} ]; then echo "r'${VIASH_PAR_MODALITY//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
|
||||
'matrix': $( if [ ! -z ${VIASH_PAR_MATRIX+x} ]; then echo "r'${VIASH_PAR_MATRIX//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
|
||||
'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OUTPUT//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
|
||||
'output_compression': $( if [ ! -z ${VIASH_PAR_OUTPUT_COMPRESSION+x} ]; then echo "r'${VIASH_PAR_OUTPUT_COMPRESSION//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
|
||||
'output_match_column': $( if [ ! -z ${VIASH_PAR_OUTPUT_MATCH_COLUMN+x} ]; then echo "r'${VIASH_PAR_OUTPUT_MATCH_COLUMN//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
|
||||
'output_fraction_column': $( if [ ! -z ${VIASH_PAR_OUTPUT_FRACTION_COLUMN+x} ]; then echo "r'${VIASH_PAR_OUTPUT_FRACTION_COLUMN//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
|
||||
'output_compression': $( if [ ! -z ${VIASH_PAR_OUTPUT_COMPRESSION+x} ]; then echo "r'${VIASH_PAR_OUTPUT_COMPRESSION//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
|
||||
'regex_pattern': $( if [ ! -z ${VIASH_PAR_REGEX_PATTERN+x} ]; then echo "r'${VIASH_PAR_REGEX_PATTERN//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi )
|
||||
}
|
||||
meta = {
|
||||
@@ -3584,9 +3598,9 @@ def main(par):
|
||||
logger.info("Fraction statistics: \\\\n%s", Series(pct_matching).describe())
|
||||
pct_matching = np.where(np.isclose(pct_matching, 0, atol=1e-6), 0, pct_matching)
|
||||
pct_matching = np.where(np.isclose(pct_matching, 1, atol=1e-6), 1, pct_matching)
|
||||
assert (
|
||||
np.logical_and(pct_matching >= 0, pct_matching <= 1)
|
||||
).all(), "Fractions are not within bounds, please report this as a bug"
|
||||
assert (np.logical_and(pct_matching >= 0, pct_matching <= 1)).all(), (
|
||||
"Fractions are not within bounds, please report this as a bug"
|
||||
)
|
||||
output_matrix = other_axis_attribute[par["matrix"]]
|
||||
logger.info(
|
||||
"Writing fractions to matrix '%s', column '%s'",
|
||||
@@ -3994,9 +4008,9 @@ meta["defaults"] = [
|
||||
// default directives
|
||||
directives: readJsonBlob('''{
|
||||
"container" : {
|
||||
"registry" : "ghcr.io",
|
||||
"image" : "openpipelines-bio/openpipeline/metadata/grep_annotation_column",
|
||||
"tag" : "2.1.0"
|
||||
"registry" : "images.viash-hub.com",
|
||||
"image" : "vsh/openpipeline/metadata/grep_annotation_column",
|
||||
"tag" : "v3.0.0"
|
||||
},
|
||||
"label" : [
|
||||
"singlecpu",
|
||||
@@ -2,7 +2,7 @@ manifest {
|
||||
name = 'metadata/grep_annotation_column'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = '2.1.2'
|
||||
version = 'v3.0.0'
|
||||
description = 'Perform a regex lookup on a column from the annotation matrices .obs or .var.\nThe annotation matrix can originate from either a modality, or all modalities (global .var or .obs).\n'
|
||||
author = 'Dries Schaumont'
|
||||
}
|
||||
@@ -6,7 +6,10 @@ process {
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// The memory a task is assinged increases with each attempt
|
||||
// uncomment the line below and adjust the value to set a global upper limit on the memory.
|
||||
// resourceLimits = [ memory: 240.Gb ]
|
||||
|
||||
// CPU resources
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
@@ -15,10 +18,10 @@ process {
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
// Memory resources
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
withLabel: lowmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 4.GB * task.attempt } }
|
||||
withLabel: midmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 25.GB * task.attempt } }
|
||||
withLabel: highmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 50.GB * task.attempt } }
|
||||
withLabel: veryhighmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 75.GB * task.attempt } }
|
||||
|
||||
// Disk space
|
||||
withLabel: lowdisk {
|
||||
@@ -43,24 +46,3 @@ process {
|
||||
// withLabel: highdisk { disk = { 200.GB * task.attempt } }
|
||||
// withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,117 @@
|
||||
{
|
||||
"$schema": "https://json-schema.org/draft/2020-12/schema",
|
||||
"title": "grep_annotation_column",
|
||||
"description": "Perform a regex lookup on a column from the annotation matrices .obs or .var.\nThe annotation matrix can originate from either a modality, or all modalities (global .var or .obs).\n",
|
||||
"type": "object",
|
||||
"$defs": {
|
||||
"inputs": {
|
||||
"title": "Inputs",
|
||||
"type": "object",
|
||||
"description": "Arguments related to the input dataset.",
|
||||
"properties": {
|
||||
"input": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"exists": true,
|
||||
"description": "Path to the input .h5mu.",
|
||||
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"sample_path\"`. "
|
||||
},
|
||||
"input_column": {
|
||||
"type": "string",
|
||||
"description": "Column to query",
|
||||
"help_text": "Type: `string`, multiple: `False`. "
|
||||
},
|
||||
"input_layer": {
|
||||
"type": "string",
|
||||
"description": "Input data to use when calculating fraction of observations that match with the query",
|
||||
"help_text": "Type: `string`, multiple: `False`. "
|
||||
},
|
||||
"modality": {
|
||||
"type": "string",
|
||||
"description": "Which modality to get the annotation matrix from.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, required, example: `\"rna\"`. "
|
||||
},
|
||||
"matrix": {
|
||||
"type": "string",
|
||||
"description": "Matrix to fetch the column from that will be searched.",
|
||||
"help_text": "Type: `string`, multiple: `False`, example: `\"var\"`, choices: ``var`, `obs``. ",
|
||||
"enum": [
|
||||
"var",
|
||||
"obs"
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
"outputs": {
|
||||
"title": "Outputs",
|
||||
"type": "object",
|
||||
"description": "Arguments related to how the output will be written.",
|
||||
"properties": {
|
||||
"output": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "Location of the output MuData file.\n",
|
||||
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
|
||||
"default": "$id.$key.output.h5mu"
|
||||
},
|
||||
"output_match_column": {
|
||||
"type": "string",
|
||||
"description": "Name of the column to write the result to.",
|
||||
"help_text": "Type: `string`, multiple: `False`, required. "
|
||||
},
|
||||
"output_fraction_column": {
|
||||
"type": "string",
|
||||
"description": "For the opposite axis, name of the column to write the fraction of \nobservations that matches to the pattern.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`. "
|
||||
},
|
||||
"output_compression": {
|
||||
"type": "string",
|
||||
"description": "Compression format to use for the output AnnData and/or Mudata objects.\nBy default no compression is applied.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, example: `\"gzip\"`, choices: ``gzip`, `lzf``. ",
|
||||
"enum": [
|
||||
"gzip",
|
||||
"lzf"
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
"query options": {
|
||||
"title": "Query options",
|
||||
"type": "object",
|
||||
"description": "Options related to the query",
|
||||
"properties": {
|
||||
"regex_pattern": {
|
||||
"type": "string",
|
||||
"description": "Regex to use to match with the input column.",
|
||||
"help_text": "Type: `string`, multiple: `False`, required, example: `\"^[mM][tT]-\"`. "
|
||||
}
|
||||
}
|
||||
},
|
||||
"nextflow input-output arguments": {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"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.",
|
||||
"properties": {
|
||||
"publish_dir": {
|
||||
"type": "string",
|
||||
"description": "Path to an output directory.",
|
||||
"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
|
||||
}
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
{
|
||||
"$ref": "#/$defs/inputs"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/outputs"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/query options"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "calculate_qc_metrics"
|
||||
namespace: "qc"
|
||||
version: "2.1.2"
|
||||
version: "v3.0.0"
|
||||
authors:
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
@@ -33,6 +33,7 @@ argument_groups:
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
description: "Which modality from the input MuData file to process. \n"
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
@@ -42,6 +43,8 @@ argument_groups:
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--layer"
|
||||
description: "Layer from modality to use as input data. If not provided the .X\
|
||||
\ attribute is used.\n"
|
||||
info: null
|
||||
example:
|
||||
- "raw_counts"
|
||||
@@ -170,7 +173,8 @@ argument_groups:
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
description: "The compression format to be used on the output h5mu object."
|
||||
description: "Compression format to use for the output AnnData and/or Mudata objects.\n\
|
||||
By default no compression is applied.\n"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
@@ -290,7 +294,8 @@ engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.11-slim"
|
||||
target_tag: "2.1.0"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v3.0.0"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
@@ -326,18 +331,21 @@ engines:
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/qc/calculate_qc_metrics/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "docker"
|
||||
engine: "docker|native"
|
||||
output: "target/nextflow/qc/calculate_qc_metrics"
|
||||
executable: "target/nextflow/qc/calculate_qc_metrics/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "a0c9522486585774f76416150f8a3291409b5363"
|
||||
git_commit: "e92e56b49125af8ef2ebb11586191a6cbf9a8457"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "2.1.1-2-ga0c95224865"
|
||||
git_tag: "0.2.0-2059-ge92e56b4"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "v3.0.0"
|
||||
summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
|
||||
description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
|
||||
\ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
|
||||
@@ -354,6 +362,10 @@ package_config:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
nextflow_labels_ci:
|
||||
- path: "src/workflows/utils/labels_ci.config"
|
||||
description: "Adds the correct memory and CPU labels when running on the Viash\
|
||||
\ Hub CI."
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
@@ -361,13 +373,14 @@ package_config:
|
||||
- ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
|
||||
)'"
|
||||
- ".version := \"2.1.2\""
|
||||
- ".engines[.type == 'docker'].target_tag := '2.1.0'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v3.0.0'"
|
||||
keywords:
|
||||
- "single-cell"
|
||||
- "multimodal"
|
||||
license: "MIT"
|
||||
organization: "openpipelines-bio"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -1,4 +1,4 @@
|
||||
// calculate_qc_metrics 2.1.2
|
||||
// calculate_qc_metrics v3.0.0
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -3035,7 +3035,7 @@ meta = [
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "calculate_qc_metrics",
|
||||
"namespace" : "qc",
|
||||
"version" : "2.1.2",
|
||||
"version" : "v3.0.0",
|
||||
"authors" : [
|
||||
{
|
||||
"name" : "Dries Schaumont",
|
||||
@@ -3081,6 +3081,7 @@ meta = [
|
||||
{
|
||||
"type" : "string",
|
||||
"name" : "--modality",
|
||||
"description" : "Which modality from the input MuData file to process. \n",
|
||||
"default" : [
|
||||
"rna"
|
||||
],
|
||||
@@ -3092,6 +3093,7 @@ meta = [
|
||||
{
|
||||
"type" : "string",
|
||||
"name" : "--layer",
|
||||
"description" : "Layer from modality to use as input data. If not provided the .X attribute is used.\n",
|
||||
"example" : [
|
||||
"raw_counts"
|
||||
],
|
||||
@@ -3234,7 +3236,7 @@ meta = [
|
||||
{
|
||||
"type" : "string",
|
||||
"name" : "--output_compression",
|
||||
"description" : "The compression format to be used on the output h5mu object.",
|
||||
"description" : "Compression format to use for the output AnnData and/or Mudata objects.\nBy default no compression is applied.\n",
|
||||
"example" : [
|
||||
"gzip"
|
||||
],
|
||||
@@ -3378,7 +3380,8 @@ meta = [
|
||||
"type" : "docker",
|
||||
"id" : "docker",
|
||||
"image" : "python:3.11-slim",
|
||||
"target_tag" : "2.1.0",
|
||||
"target_registry" : "images.viash-hub.com",
|
||||
"target_tag" : "v3.0.0",
|
||||
"namespace_separator" : "/",
|
||||
"setup" : [
|
||||
{
|
||||
@@ -3430,20 +3433,25 @@ meta = [
|
||||
"upgrade" : true
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"type" : "native",
|
||||
"id" : "native"
|
||||
}
|
||||
],
|
||||
"build_info" : {
|
||||
"config" : "/home/runner/work/openpipeline/openpipeline/src/qc/calculate_qc_metrics/config.vsh.yaml",
|
||||
"config" : "/workdir/root/repo/src/qc/calculate_qc_metrics/config.vsh.yaml",
|
||||
"runner" : "nextflow",
|
||||
"engine" : "docker",
|
||||
"output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/calculate_qc_metrics",
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/qc/calculate_qc_metrics",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "a0c9522486585774f76416150f8a3291409b5363",
|
||||
"git_commit" : "e92e56b49125af8ef2ebb11586191a6cbf9a8457",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline",
|
||||
"git_tag" : "2.1.1-2-ga0c95224865"
|
||||
"git_tag" : "0.2.0-2059-ge92e56b4"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "openpipeline",
|
||||
"version" : "v3.0.0",
|
||||
"summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
|
||||
"description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n",
|
||||
"info" : {
|
||||
@@ -3453,22 +3461,29 @@ meta = [
|
||||
"path" : "s3://openpipelines-data",
|
||||
"dest" : "resources_test"
|
||||
}
|
||||
],
|
||||
"nextflow_labels_ci" : [
|
||||
{
|
||||
"path" : "src/workflows/utils/labels_ci.config",
|
||||
"description" : "Adds the correct memory and CPU labels when running on the Viash Hub CI."
|
||||
}
|
||||
]
|
||||
},
|
||||
"viash_version" : "0.9.4",
|
||||
"source" : "/home/runner/work/openpipeline/openpipeline/src",
|
||||
"target" : "/home/runner/work/openpipeline/openpipeline/target",
|
||||
"source" : "/workdir/root/repo/src",
|
||||
"target" : "/workdir/root/repo/target",
|
||||
"config_mods" : [
|
||||
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
|
||||
".version := \\"2.1.2\\"",
|
||||
".engines[.type == 'docker'].target_tag := '2.1.0'"
|
||||
".engines += { type: \\"native\\" }",
|
||||
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
|
||||
".engines[.type == 'docker'].target_tag := 'v3.0.0'"
|
||||
],
|
||||
"keywords" : [
|
||||
"single-cell",
|
||||
"multimodal"
|
||||
],
|
||||
"license" : "MIT",
|
||||
"organization" : "openpipelines-bio",
|
||||
"organization" : "vsh",
|
||||
"links" : {
|
||||
"repository" : "https://github.com/openpipelines-bio/openpipeline",
|
||||
"docker_registry" : "ghcr.io",
|
||||
@@ -4090,9 +4105,9 @@ meta["defaults"] = [
|
||||
// default directives
|
||||
directives: readJsonBlob('''{
|
||||
"container" : {
|
||||
"registry" : "ghcr.io",
|
||||
"image" : "openpipelines-bio/openpipeline/qc/calculate_qc_metrics",
|
||||
"tag" : "2.1.0"
|
||||
"registry" : "images.viash-hub.com",
|
||||
"image" : "vsh/openpipeline/qc/calculate_qc_metrics",
|
||||
"tag" : "v3.0.0"
|
||||
},
|
||||
"label" : [
|
||||
"singlecpu",
|
||||
@@ -2,7 +2,7 @@ manifest {
|
||||
name = 'qc/calculate_qc_metrics'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = '2.1.2'
|
||||
version = 'v3.0.0'
|
||||
description = 'Add basic quality control metrics to an .h5mu file.\n\nThe metrics are comparable to what scanpy.pp.calculate_qc_metrics output,\nalthough they have slightly different names:\n\nVar metrics (name in this component -> name in scanpy):\n - pct_dropout -> pct_dropout_by_{expr_type}\n - num_nonzero_obs -> n_cells_by_{expr_type}\n - obs_mean -> mean_{expr_type}\n - total_counts -> total_{expr_type}\n\n Obs metrics:\n - num_nonzero_vars -> n_genes_by_{expr_type}\n - pct_{var_qc_metrics} -> pct_{expr_type}_{qc_var}\n - total_counts_{var_qc_metrics} -> total_{expr_type}_{qc_var}\n - pct_of_counts_in_top_{top_n_vars}_vars -> pct_{expr_type}_in_top_{n}_{var_type}\n - total_counts -> total_{expr_type}\n \n'
|
||||
author = 'Dries Schaumont'
|
||||
}
|
||||
@@ -6,7 +6,10 @@ process {
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// The memory a task is assinged increases with each attempt
|
||||
// uncomment the line below and adjust the value to set a global upper limit on the memory.
|
||||
// resourceLimits = [ memory: 240.Gb ]
|
||||
|
||||
// CPU resources
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
@@ -15,10 +18,10 @@ process {
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
// Memory resources
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
withLabel: lowmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 4.GB * task.attempt } }
|
||||
withLabel: midmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 25.GB * task.attempt } }
|
||||
withLabel: highmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 50.GB * task.attempt } }
|
||||
withLabel: veryhighmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 75.GB * task.attempt } }
|
||||
|
||||
// Disk space
|
||||
withLabel: lowdisk {
|
||||
@@ -43,24 +46,3 @@ process {
|
||||
// withLabel: highdisk { disk = { 200.GB * task.attempt } }
|
||||
// withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,156 @@
|
||||
{
|
||||
"$schema": "https://json-schema.org/draft/2020-12/schema",
|
||||
"title": "calculate_qc_metrics",
|
||||
"description": "Add basic quality control metrics to an .h5mu file.\n\nThe metrics are comparable to what scanpy.pp.calculate_qc_metrics output,\nalthough they have slightly different names:\n\nVar metrics (name in this component -> name in scanpy):\n - pct_dropout -> pct_dropout_by_{expr_type}\n - num_nonzero_obs -> n_cells_by_{expr_type}\n - obs_mean -> mean_{expr_type}\n - total_counts -> total_{expr_type}\n\n Obs metrics:\n - num_nonzero_vars -> n_genes_by_{expr_type}\n - pct_{var_qc_metrics} -> pct_{expr_type}_{qc_var}\n - total_counts_{var_qc_metrics} -> total_{expr_type}_{qc_var}\n - pct_of_counts_in_top_{top_n_vars}_vars -> pct_{expr_type}_in_top_{n}_{var_type}\n - total_counts -> total_{expr_type}\n \n",
|
||||
"type": "object",
|
||||
"$defs": {
|
||||
"inputs": {
|
||||
"title": "Inputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"input": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"exists": true,
|
||||
"description": "Input h5mu file",
|
||||
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.h5mu\"`. "
|
||||
},
|
||||
"modality": {
|
||||
"type": "string",
|
||||
"description": "Which modality from the input MuData file to process",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"rna\"`. ",
|
||||
"default": "rna"
|
||||
},
|
||||
"layer": {
|
||||
"type": "string",
|
||||
"description": "Layer from modality to use as input data",
|
||||
"help_text": "Type: `string`, multiple: `False`, example: `\"raw_counts\"`. "
|
||||
}
|
||||
}
|
||||
},
|
||||
"outputs": {
|
||||
"title": "Outputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"output": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "Output h5mu file.",
|
||||
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
|
||||
"default": "$id.$key.output.h5mu"
|
||||
},
|
||||
"output_compression": {
|
||||
"type": "string",
|
||||
"description": "Compression format to use for the output AnnData and/or Mudata objects.\nBy default no compression is applied.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, example: `\"gzip\"`, choices: ``gzip`, `lzf``. ",
|
||||
"enum": [
|
||||
"gzip",
|
||||
"lzf"
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
"metrics added to .obs": {
|
||||
"title": "Metrics added to .obs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"var_qc_metrics": {
|
||||
"type": "array",
|
||||
"items": {
|
||||
"type": "string"
|
||||
},
|
||||
"description": "Keys to select a boolean (containing only True or False) column from .var.\nFor each cell, calculate the proportion of total values for genes which are labeled 'True', \ncompared to the total sum of the values for all genes.\n",
|
||||
"help_text": "Type: `string`, multiple: `True`, example: `[\"ercc,highly_variable,mitochondrial\"]`. "
|
||||
},
|
||||
"var_qc_metrics_fill_na_value": {
|
||||
"type": "boolean",
|
||||
"description": "Fill any 'NA' values found in the columns specified with --var_qc_metrics to 'True' or 'False'.\nas False.\n",
|
||||
"help_text": "Type: `boolean`, multiple: `False`. "
|
||||
},
|
||||
"top_n_vars": {
|
||||
"type": "array",
|
||||
"items": {
|
||||
"type": "integer"
|
||||
},
|
||||
"description": "Number of top vars to be used to calculate cumulative proportions.\nIf not specified, proportions are not calculated",
|
||||
"help_text": "Type: `integer`, multiple: `True`. "
|
||||
},
|
||||
"output_obs_num_nonzero_vars": {
|
||||
"type": "string",
|
||||
"description": "Name of column in .obs describing, for each observation, the number of stored values\n(including explicit zeroes)",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"num_nonzero_vars\"`. ",
|
||||
"default": "num_nonzero_vars"
|
||||
},
|
||||
"output_obs_total_counts_vars": {
|
||||
"type": "string",
|
||||
"description": "Name of the column for .obs describing, for each observation (row),\nthe sum of the stored values in the columns.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"total_counts\"`. ",
|
||||
"default": "total_counts"
|
||||
}
|
||||
}
|
||||
},
|
||||
"metrics added to .var": {
|
||||
"title": "Metrics added to .var",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"output_var_num_nonzero_obs": {
|
||||
"type": "string",
|
||||
"description": "Name of column describing, for each feature, the number of stored values\n(including explicit zeroes)",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"num_nonzero_obs\"`. ",
|
||||
"default": "num_nonzero_obs"
|
||||
},
|
||||
"output_var_total_counts_obs": {
|
||||
"type": "string",
|
||||
"description": "Name of the column in .var describing, for each feature (column),\nthe sum of the stored values in the rows.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"total_counts\"`. ",
|
||||
"default": "total_counts"
|
||||
},
|
||||
"output_var_obs_mean": {
|
||||
"type": "string",
|
||||
"description": "Name of the column in .obs providing the mean of the values in each row.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"obs_mean\"`. ",
|
||||
"default": "obs_mean"
|
||||
},
|
||||
"output_var_pct_dropout": {
|
||||
"type": "string",
|
||||
"description": "Name of the column in .obs providing for each feature the percentage of\nobservations the feature does not appear on (i.e",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"pct_dropout\"`. ",
|
||||
"default": "pct_dropout"
|
||||
}
|
||||
}
|
||||
},
|
||||
"nextflow input-output arguments": {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"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.",
|
||||
"properties": {
|
||||
"publish_dir": {
|
||||
"type": "string",
|
||||
"description": "Path to an output directory.",
|
||||
"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
|
||||
}
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
{
|
||||
"$ref": "#/$defs/inputs"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/outputs"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/metrics added to .obs"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/metrics added to .var"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "qc"
|
||||
namespace: "workflows/qc"
|
||||
version: "2.1.2"
|
||||
version: "v3.0.0"
|
||||
authors:
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
@@ -354,6 +354,9 @@ runners:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/workflows/qc/qc/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
@@ -361,14 +364,15 @@ build_info:
|
||||
output: "target/nextflow/workflows/qc/qc"
|
||||
executable: "target/nextflow/workflows/qc/qc/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "a0c9522486585774f76416150f8a3291409b5363"
|
||||
git_commit: "e92e56b49125af8ef2ebb11586191a6cbf9a8457"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "2.1.1-2-ga0c95224865"
|
||||
git_tag: "0.2.0-2059-ge92e56b4"
|
||||
dependencies:
|
||||
- "target/nextflow/metadata/grep_annotation_column"
|
||||
- "target/nextflow/qc/calculate_qc_metrics"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "v3.0.0"
|
||||
summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
|
||||
description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
|
||||
\ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
|
||||
@@ -385,6 +389,10 @@ package_config:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
nextflow_labels_ci:
|
||||
- path: "src/workflows/utils/labels_ci.config"
|
||||
description: "Adds the correct memory and CPU labels when running on the Viash\
|
||||
\ Hub CI."
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
@@ -392,12 +400,14 @@ package_config:
|
||||
- ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
|
||||
)'"
|
||||
- ".version := \"2.1.2\""
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v3.0.0'"
|
||||
keywords:
|
||||
- "single-cell"
|
||||
- "multimodal"
|
||||
license: "MIT"
|
||||
organization: "openpipelines-bio"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -1,4 +1,4 @@
|
||||
// qc 2.1.2
|
||||
// qc v3.0.0
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -3035,7 +3035,7 @@ meta = [
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "qc",
|
||||
"namespace" : "workflows/qc",
|
||||
"version" : "2.1.2",
|
||||
"version" : "v3.0.0",
|
||||
"authors" : [
|
||||
{
|
||||
"name" : "Dries Schaumont",
|
||||
@@ -3466,17 +3466,18 @@ meta = [
|
||||
}
|
||||
],
|
||||
"build_info" : {
|
||||
"config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml",
|
||||
"config" : "/workdir/root/repo/src/workflows/qc/qc/config.vsh.yaml",
|
||||
"runner" : "nextflow",
|
||||
"engine" : "native",
|
||||
"output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/qc/qc",
|
||||
"output" : "/workdir/root/repo/target/nextflow/workflows/qc/qc",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "a0c9522486585774f76416150f8a3291409b5363",
|
||||
"git_commit" : "e92e56b49125af8ef2ebb11586191a6cbf9a8457",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline",
|
||||
"git_tag" : "2.1.1-2-ga0c95224865"
|
||||
"git_tag" : "0.2.0-2059-ge92e56b4"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "openpipeline",
|
||||
"version" : "v3.0.0",
|
||||
"summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
|
||||
"description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n",
|
||||
"info" : {
|
||||
@@ -3486,21 +3487,29 @@ meta = [
|
||||
"path" : "s3://openpipelines-data",
|
||||
"dest" : "resources_test"
|
||||
}
|
||||
],
|
||||
"nextflow_labels_ci" : [
|
||||
{
|
||||
"path" : "src/workflows/utils/labels_ci.config",
|
||||
"description" : "Adds the correct memory and CPU labels when running on the Viash Hub CI."
|
||||
}
|
||||
]
|
||||
},
|
||||
"viash_version" : "0.9.4",
|
||||
"source" : "/home/runner/work/openpipeline/openpipeline/src",
|
||||
"target" : "/home/runner/work/openpipeline/openpipeline/target",
|
||||
"source" : "/workdir/root/repo/src",
|
||||
"target" : "/workdir/root/repo/target",
|
||||
"config_mods" : [
|
||||
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
|
||||
".version := \\"2.1.2\\""
|
||||
".engines += { type: \\"native\\" }",
|
||||
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
|
||||
".engines[.type == 'docker'].target_tag := 'v3.0.0'"
|
||||
],
|
||||
"keywords" : [
|
||||
"single-cell",
|
||||
"multimodal"
|
||||
],
|
||||
"license" : "MIT",
|
||||
"organization" : "openpipelines-bio",
|
||||
"organization" : "vsh",
|
||||
"links" : {
|
||||
"repository" : "https://github.com/openpipelines-bio/openpipeline",
|
||||
"docker_registry" : "ghcr.io",
|
||||
@@ -2,7 +2,7 @@ manifest {
|
||||
name = 'workflows/qc/qc'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = '2.1.2'
|
||||
version = 'v3.0.0'
|
||||
description = 'A pipeline to add basic qc statistics to a MuData '
|
||||
author = 'Dries Schaumont'
|
||||
}
|
||||
@@ -6,7 +6,10 @@ process {
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// The memory a task is assinged increases with each attempt
|
||||
// uncomment the line below and adjust the value to set a global upper limit on the memory.
|
||||
// resourceLimits = [ memory: 240.Gb ]
|
||||
|
||||
// CPU resources
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
@@ -15,10 +18,10 @@ process {
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
// Memory resources
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
withLabel: lowmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 4.GB * task.attempt } }
|
||||
withLabel: midmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 25.GB * task.attempt } }
|
||||
withLabel: highmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 50.GB * task.attempt } }
|
||||
withLabel: veryhighmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 75.GB * task.attempt } }
|
||||
|
||||
// Disk space
|
||||
withLabel: lowdisk {
|
||||
@@ -43,24 +46,3 @@ process {
|
||||
// withLabel: highdisk { disk = { 200.GB * task.attempt } }
|
||||
// withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,190 @@
|
||||
{
|
||||
"$schema": "https://json-schema.org/draft/2020-12/schema",
|
||||
"title": "qc",
|
||||
"description": "A pipeline to add basic qc statistics to a MuData ",
|
||||
"type": "object",
|
||||
"$defs": {
|
||||
"inputs": {
|
||||
"title": "Inputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"id": {
|
||||
"type": "string",
|
||||
"description": "ID of the sample.",
|
||||
"help_text": "Type: `string`, multiple: `False`, required, example: `\"foo\"`. "
|
||||
},
|
||||
"input": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"exists": true,
|
||||
"description": "Path to the sample.",
|
||||
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.h5mu\"`. "
|
||||
},
|
||||
"modality": {
|
||||
"type": "string",
|
||||
"description": "Which modality to process.",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"rna\"`. ",
|
||||
"default": "rna"
|
||||
},
|
||||
"layer": {
|
||||
"type": "string",
|
||||
"description": "Layer to calculate qc metrics for.",
|
||||
"help_text": "Type: `string`, multiple: `False`, example: `\"raw_counts\"`. "
|
||||
}
|
||||
}
|
||||
},
|
||||
"outputs": {
|
||||
"title": "Outputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"output": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "Destination path to the output.",
|
||||
"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
|
||||
"default": "$id.$key.output.h5mu"
|
||||
}
|
||||
}
|
||||
},
|
||||
"mitochondrial & ribosomal gene detection": {
|
||||
"title": "Mitochondrial & Ribosomal Gene Detection",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"var_gene_names": {
|
||||
"type": "string",
|
||||
"description": ".var column name to be used to detect mitochondrial/ribosomal genes instead of .var_names (default if not set).\nGene names matching with the regex value from --mitochondrial_gene_regex or --ribosomal_gene_regex will be \nidentified as mitochondrial or ribosomal genes, respectively.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, example: `\"gene_symbol\"`. "
|
||||
},
|
||||
"var_name_mitochondrial_genes": {
|
||||
"type": "string",
|
||||
"description": "In which .var slot to store a boolean array corresponding the mitochondrial genes.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`. "
|
||||
},
|
||||
"obs_name_mitochondrial_fraction": {
|
||||
"type": "string",
|
||||
"description": ".Obs slot to store the fraction of reads found to be mitochondrial",
|
||||
"help_text": "Type: `string`, multiple: `False`. "
|
||||
},
|
||||
"mitochondrial_gene_regex": {
|
||||
"type": "string",
|
||||
"description": "Regex string that identifies mitochondrial genes from --var_gene_names.\nBy default will detect human and mouse mitochondrial genes from a gene symbol.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"^[mM][tT]-\"`. ",
|
||||
"default": "^[mM][tT]-"
|
||||
},
|
||||
"var_name_ribosomal_genes": {
|
||||
"type": "string",
|
||||
"description": "In which .var slot to store a boolean array corresponding the ribosomal genes.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`. "
|
||||
},
|
||||
"obs_name_ribosomal_fraction": {
|
||||
"type": "string",
|
||||
"description": "When specified, write the fraction of counts originating from ribosomal genes \n(based on --ribosomal_gene_regex) to an .obs column with the specified name.\nRequires --var_name_ribosomal_genes.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`. "
|
||||
},
|
||||
"ribosomal_gene_regex": {
|
||||
"type": "string",
|
||||
"description": "Regex string that identifies ribosomal genes from --var_gene_names.\nBy default will detect human and mouse ribosomal genes from a gene symbol.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"^[Mm]?[Rr][Pp][LlSs]\"`. ",
|
||||
"default": "^[Mm]?[Rr][Pp][LlSs]"
|
||||
}
|
||||
}
|
||||
},
|
||||
"qc metrics calculation options": {
|
||||
"title": "QC metrics calculation options",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"var_qc_metrics": {
|
||||
"type": "array",
|
||||
"items": {
|
||||
"type": "string"
|
||||
},
|
||||
"description": "Keys to select a boolean (containing only True or False) column from .var.\nFor each cell, calculate the proportion of total values for genes which are labeled 'True', \ncompared to the total sum of the values for all genes",
|
||||
"help_text": "Type: `string`, multiple: `True`, example: `[\"ercc,highly_variable\"]`. "
|
||||
},
|
||||
"top_n_vars": {
|
||||
"type": "array",
|
||||
"items": {
|
||||
"type": "integer"
|
||||
},
|
||||
"description": "Number of top vars to be used to calculate cumulative proportions.\nIf not specified, proportions are not calculated",
|
||||
"help_text": "Type: `integer`, multiple: `True`, default: `[50,100,200,500]`. ",
|
||||
"default": [
|
||||
50,
|
||||
100,
|
||||
200,
|
||||
500
|
||||
]
|
||||
},
|
||||
"output_obs_num_nonzero_vars": {
|
||||
"type": "string",
|
||||
"description": "Name of column in .obs describing, for each observation, the number of stored values\n(including explicit zeroes)",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"num_nonzero_vars\"`. ",
|
||||
"default": "num_nonzero_vars"
|
||||
},
|
||||
"output_obs_total_counts_vars": {
|
||||
"type": "string",
|
||||
"description": "Name of the column for .obs describing, for each observation (row),\nthe sum of the stored values in the columns.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"total_counts\"`. ",
|
||||
"default": "total_counts"
|
||||
},
|
||||
"output_var_num_nonzero_obs": {
|
||||
"type": "string",
|
||||
"description": "Name of column describing, for each feature, the number of stored values\n(including explicit zeroes)",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"num_nonzero_obs\"`. ",
|
||||
"default": "num_nonzero_obs"
|
||||
},
|
||||
"output_var_total_counts_obs": {
|
||||
"type": "string",
|
||||
"description": "Name of the column in .var describing, for each feature (column),\nthe sum of the stored values in the rows.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"total_counts\"`. ",
|
||||
"default": "total_counts"
|
||||
},
|
||||
"output_var_obs_mean": {
|
||||
"type": "string",
|
||||
"description": "Name of the column in .obs providing the mean of the values in each row.\n",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"obs_mean\"`. ",
|
||||
"default": "obs_mean"
|
||||
},
|
||||
"output_var_pct_dropout": {
|
||||
"type": "string",
|
||||
"description": "Name of the column in .obs providing for each feature the percentage of\nobservations the feature does not appear on (i.e",
|
||||
"help_text": "Type: `string`, multiple: `False`, default: `\"pct_dropout\"`. ",
|
||||
"default": "pct_dropout"
|
||||
}
|
||||
}
|
||||
},
|
||||
"nextflow input-output arguments": {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"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.",
|
||||
"properties": {
|
||||
"publish_dir": {
|
||||
"type": "string",
|
||||
"description": "Path to an output directory.",
|
||||
"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
|
||||
}
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
{
|
||||
"$ref": "#/$defs/inputs"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/outputs"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/mitochondrial & ribosomal gene detection"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/qc metrics calculation options"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -6,7 +6,10 @@ process {
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// The memory a task is assinged increases with each attempt
|
||||
// uncomment the line below and adjust the value to set a global upper limit on the memory.
|
||||
// resourceLimits = [ memory: 240.Gb ]
|
||||
|
||||
// CPU resources
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
@@ -15,10 +18,10 @@ process {
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
// Memory resources
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
withLabel: lowmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 4.GB * task.attempt } }
|
||||
withLabel: midmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 25.GB * task.attempt } }
|
||||
withLabel: highmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 50.GB * task.attempt } }
|
||||
withLabel: veryhighmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 75.GB * task.attempt } }
|
||||
|
||||
// Disk space
|
||||
withLabel: lowdisk {
|
||||
@@ -43,24 +46,3 @@ process {
|
||||
// withLabel: highdisk { disk = { 200.GB * task.attempt } }
|
||||
// withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -174,10 +174,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -290,7 +290,7 @@ build_info:
|
||||
output: "target/executable/convert/from_cells2stats_to_h5mu"
|
||||
executable: "target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -301,10 +301,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component convert from_cells2stats_to_h5mu"
|
||||
LABEL org.opencontainers.image.created="2025-08-22T15:23:01Z"
|
||||
LABEL org.opencontainers.image.created="2025-08-23T07:09:21Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
LABEL org.opencontainers.image.revision="48abb52b6651d453d43f74521cda027916395063"
|
||||
LABEL org.opencontainers.image.revision="3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
LABEL org.opencontainers.image.version="0.1.0"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -102,10 +102,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -225,7 +225,7 @@ build_info:
|
||||
output: "target/executable/convert/from_cosmx_to_h5mu"
|
||||
executable: "target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -236,10 +236,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_h5mu"
|
||||
LABEL org.opencontainers.image.created="2025-08-22T15:23:03Z"
|
||||
LABEL org.opencontainers.image.created="2025-08-23T07:09:22Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
LABEL org.opencontainers.image.revision="48abb52b6651d453d43f74521cda027916395063"
|
||||
LABEL org.opencontainers.image.revision="3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
LABEL org.opencontainers.image.version="0.1.0"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -120,10 +120,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -232,7 +232,7 @@ build_info:
|
||||
output: "target/executable/convert/from_cosmx_to_spatialexperiment"
|
||||
executable: "target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -243,10 +243,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_spatialexperiment"
|
||||
LABEL org.opencontainers.image.created="2025-08-22T15:23:02Z"
|
||||
LABEL org.opencontainers.image.created="2025-08-23T07:09:21Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
LABEL org.opencontainers.image.revision="48abb52b6651d453d43f74521cda027916395063"
|
||||
LABEL org.opencontainers.image.revision="3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
LABEL org.opencontainers.image.version="0.1.0"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -89,10 +89,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -224,7 +224,7 @@ build_info:
|
||||
output: "target/executable/convert/from_h5mu_to_spatialexperiment"
|
||||
executable: "target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -235,10 +235,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -458,9 +458,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_spatialexperiment"
|
||||
LABEL org.opencontainers.image.created="2025-08-22T15:23:02Z"
|
||||
LABEL org.opencontainers.image.created="2025-08-23T07:09:22Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
LABEL org.opencontainers.image.revision="48abb52b6651d453d43f74521cda027916395063"
|
||||
LABEL org.opencontainers.image.revision="3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
LABEL org.opencontainers.image.version="0.1.0"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -98,10 +98,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -220,7 +220,7 @@ build_info:
|
||||
output: "target/executable/convert/from_spatialdata_to_h5mu"
|
||||
executable: "target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -231,10 +231,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component convert from_spatialdata_to_h5mu"
|
||||
LABEL org.opencontainers.image.created="2025-08-22T15:23:02Z"
|
||||
LABEL org.opencontainers.image.created="2025-08-23T07:09:21Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
LABEL org.opencontainers.image.revision="48abb52b6651d453d43f74521cda027916395063"
|
||||
LABEL org.opencontainers.image.revision="3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
LABEL org.opencontainers.image.version="0.1.0"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -116,10 +116,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -233,7 +233,7 @@ build_info:
|
||||
output: "target/executable/convert/from_xenium_to_h5mu"
|
||||
executable: "target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -244,10 +244,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_h5mu"
|
||||
LABEL org.opencontainers.image.created="2025-08-22T15:23:02Z"
|
||||
LABEL org.opencontainers.image.created="2025-08-23T07:09:21Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
LABEL org.opencontainers.image.revision="48abb52b6651d453d43f74521cda027916395063"
|
||||
LABEL org.opencontainers.image.revision="3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
LABEL org.opencontainers.image.version="0.1.0"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -196,10 +196,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -314,7 +314,7 @@ build_info:
|
||||
output: "target/executable/convert/from_xenium_to_spatialdata"
|
||||
executable: "target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -325,10 +325,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialdata"
|
||||
LABEL org.opencontainers.image.created="2025-08-22T15:23:02Z"
|
||||
LABEL org.opencontainers.image.created="2025-08-23T07:09:22Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
LABEL org.opencontainers.image.revision="48abb52b6651d453d43f74521cda027916395063"
|
||||
LABEL org.opencontainers.image.revision="3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
LABEL org.opencontainers.image.version="0.1.0"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -110,10 +110,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -222,7 +222,7 @@ build_info:
|
||||
output: "target/executable/convert/from_xenium_to_spatialexperiment"
|
||||
executable: "target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -233,10 +233,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialexperiment"
|
||||
LABEL org.opencontainers.image.created="2025-08-22T15:23:02Z"
|
||||
LABEL org.opencontainers.image.created="2025-08-23T07:09:21Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
LABEL org.opencontainers.image.revision="48abb52b6651d453d43f74521cda027916395063"
|
||||
LABEL org.opencontainers.image.revision="3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
LABEL org.opencontainers.image.version="0.1.0"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -109,10 +109,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -227,7 +227,7 @@ build_info:
|
||||
output: "target/executable/filter/subset_cosmx"
|
||||
executable: "target/executable/filter/subset_cosmx/subset_cosmx"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -238,10 +238,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component filter subset_cosmx"
|
||||
LABEL org.opencontainers.image.created="2025-08-22T15:23:01Z"
|
||||
LABEL org.opencontainers.image.created="2025-08-23T07:09:21Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
LABEL org.opencontainers.image.revision="48abb52b6651d453d43f74521cda027916395063"
|
||||
LABEL org.opencontainers.image.revision="3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
LABEL org.opencontainers.image.version="0.1.0"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -326,10 +326,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
keywords:
|
||||
- "spaceranger"
|
||||
links:
|
||||
@@ -426,7 +426,7 @@ build_info:
|
||||
output: "target/executable/mapping/spaceranger_count"
|
||||
executable: "target/executable/mapping/spaceranger_count/spaceranger_count"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -437,10 +437,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -453,9 +453,9 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/*
|
||||
|
||||
LABEL org.opencontainers.image.authors="Jakub Majercik"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count"
|
||||
LABEL org.opencontainers.image.created="2025-08-22T15:23:03Z"
|
||||
LABEL org.opencontainers.image.created="2025-08-23T07:09:22Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
LABEL org.opencontainers.image.revision="48abb52b6651d453d43f74521cda027916395063"
|
||||
LABEL org.opencontainers.image.revision="3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
LABEL org.opencontainers.image.version="0.1.0"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -174,10 +174,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -290,7 +290,7 @@ build_info:
|
||||
output: "target/nextflow/convert/from_cells2stats_to_h5mu"
|
||||
executable: "target/nextflow/convert/from_cells2stats_to_h5mu/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -301,10 +301,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3239,10 +3239,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"links" : {
|
||||
@@ -3382,7 +3382,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3399,10 +3399,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
|
||||
@@ -102,10 +102,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -225,7 +225,7 @@ build_info:
|
||||
output: "target/nextflow/convert/from_cosmx_to_h5mu"
|
||||
executable: "target/nextflow/convert/from_cosmx_to_h5mu/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -236,10 +236,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3177,10 +3177,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"links" : {
|
||||
@@ -3331,7 +3331,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3348,10 +3348,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
|
||||
@@ -120,10 +120,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -232,7 +232,7 @@ build_info:
|
||||
output: "target/nextflow/convert/from_cosmx_to_spatialexperiment"
|
||||
executable: "target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -243,10 +243,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3183,10 +3183,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"links" : {
|
||||
@@ -3322,7 +3322,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3339,10 +3339,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
|
||||
@@ -89,10 +89,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -224,7 +224,7 @@ build_info:
|
||||
output: "target/nextflow/convert/from_h5mu_to_spatialexperiment"
|
||||
executable: "target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -235,10 +235,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3160,10 +3160,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"links" : {
|
||||
@@ -3332,7 +3332,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_spatialexperiment",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3349,10 +3349,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
|
||||
@@ -98,10 +98,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -220,7 +220,7 @@ build_info:
|
||||
output: "target/nextflow/convert/from_spatialdata_to_h5mu"
|
||||
executable: "target/nextflow/convert/from_spatialdata_to_h5mu/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -231,10 +231,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3177,10 +3177,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"links" : {
|
||||
@@ -3330,7 +3330,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3347,10 +3347,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
|
||||
@@ -116,10 +116,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -233,7 +233,7 @@ build_info:
|
||||
output: "target/nextflow/convert/from_xenium_to_h5mu"
|
||||
executable: "target/nextflow/convert/from_xenium_to_h5mu/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -244,10 +244,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3187,10 +3187,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"links" : {
|
||||
@@ -3331,7 +3331,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3348,10 +3348,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
|
||||
@@ -196,10 +196,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -314,7 +314,7 @@ build_info:
|
||||
output: "target/nextflow/convert/from_xenium_to_spatialdata"
|
||||
executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -325,10 +325,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3276,10 +3276,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"links" : {
|
||||
@@ -3425,7 +3425,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3442,10 +3442,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
|
||||
@@ -110,10 +110,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -222,7 +222,7 @@ build_info:
|
||||
output: "target/nextflow/convert/from_xenium_to_spatialexperiment"
|
||||
executable: "target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -233,10 +233,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3172,10 +3172,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"links" : {
|
||||
@@ -3311,7 +3311,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3328,10 +3328,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
|
||||
@@ -109,10 +109,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -227,7 +227,7 @@ build_info:
|
||||
output: "target/nextflow/filter/subset_cosmx"
|
||||
executable: "target/nextflow/filter/subset_cosmx/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -238,10 +238,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3184,10 +3184,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"links" : {
|
||||
@@ -3333,7 +3333,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3350,10 +3350,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
|
||||
@@ -326,10 +326,10 @@ scope:
|
||||
image: "public"
|
||||
target: "public"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
keywords:
|
||||
- "spaceranger"
|
||||
links:
|
||||
@@ -426,7 +426,7 @@ build_info:
|
||||
output: "target/nextflow/mapping/spaceranger_count"
|
||||
executable: "target/nextflow/mapping/spaceranger_count/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
@@ -437,10 +437,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3429,10 +3429,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"keywords" : [
|
||||
@@ -3548,7 +3548,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3565,10 +3565,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
|
||||
@@ -559,10 +559,10 @@ dependencies:
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "disable-scrublet_build"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
- type: "github"
|
||||
name: "openpipeline_scrublet"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
@@ -644,7 +644,7 @@ build_info:
|
||||
output: "target/nextflow/workflows/multiomics/spatial_process_samples"
|
||||
executable: "target/nextflow/workflows/multiomics/spatial_process_samples/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
dependencies:
|
||||
- "target/dependencies/github/openpipelines-bio/openpipeline/disable-scrublet_build/nextflow/workflows/multiomics/process_samples"
|
||||
@@ -657,10 +657,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3713,10 +3713,10 @@ meta = [
|
||||
],
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
},
|
||||
{
|
||||
"type" : "github",
|
||||
@@ -3813,7 +3813,7 @@ meta = [
|
||||
"engine" : "native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3830,10 +3830,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
|
||||
@@ -302,14 +302,14 @@ dependencies:
|
||||
- name: "workflows/qc/qc"
|
||||
alias: "spatial_qc_workflow"
|
||||
repository:
|
||||
type: "github"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
type: "vsh"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
docker_registry: "ghcr.io"
|
||||
@@ -387,10 +387,10 @@ build_info:
|
||||
output: "target/nextflow/workflows/qc/spatial_qc"
|
||||
executable: "target/nextflow/workflows/qc/spatial_qc/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "48abb52b6651d453d43f74521cda027916395063"
|
||||
git_commit: "3947a0286c4d48e458ff0997cd8cff13da377f42"
|
||||
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
dependencies:
|
||||
- "target/dependencies/github/openpipelines-bio/openpipeline/2.1.2/nextflow/workflows/qc/qc"
|
||||
- "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/qc/qc"
|
||||
package_config:
|
||||
name: "openpipeline_spatial"
|
||||
version: "0.1.0"
|
||||
@@ -400,10 +400,10 @@ package_config:
|
||||
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
|
||||
dest: "resources_test"
|
||||
repositories:
|
||||
- type: "github"
|
||||
- type: "vsh"
|
||||
name: "openpipeline"
|
||||
repo: "openpipelines-bio/openpipeline"
|
||||
tag: "2.1.2"
|
||||
repo: "openpipeline"
|
||||
tag: "v3.0.0"
|
||||
viash_version: "0.9.4"
|
||||
source: "src"
|
||||
target: "target"
|
||||
|
||||
@@ -3403,18 +3403,18 @@ meta = [
|
||||
"name" : "workflows/qc/qc",
|
||||
"alias" : "spatial_qc_workflow",
|
||||
"repository" : {
|
||||
"type" : "github",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"type" : "vsh",
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
}
|
||||
],
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"links" : {
|
||||
@@ -3505,7 +3505,7 @@ meta = [
|
||||
"engine" : "native",
|
||||
"output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "48abb52b6651d453d43f74521cda027916395063",
|
||||
"git_commit" : "3947a0286c4d48e458ff0997cd8cff13da377f42",
|
||||
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
|
||||
},
|
||||
"package_config" : {
|
||||
@@ -3522,10 +3522,10 @@ meta = [
|
||||
},
|
||||
"repositories" : [
|
||||
{
|
||||
"type" : "github",
|
||||
"type" : "vsh",
|
||||
"name" : "openpipeline",
|
||||
"repo" : "openpipelines-bio/openpipeline",
|
||||
"tag" : "2.1.2"
|
||||
"repo" : "openpipeline",
|
||||
"tag" : "v3.0.0"
|
||||
}
|
||||
],
|
||||
"viash_version" : "0.9.4",
|
||||
@@ -3548,7 +3548,7 @@ meta = [
|
||||
|
||||
// resolve dependencies dependencies (if any)
|
||||
meta["root_dir"] = getRootDir()
|
||||
include { qc as spatial_qc_workflow_viashalias } from "${meta.root_dir}/dependencies/github/openpipelines-bio/openpipeline/2.1.2/nextflow/workflows/qc/qc/main.nf"
|
||||
include { qc as spatial_qc_workflow_viashalias } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/qc/qc/main.nf"
|
||||
spatial_qc_workflow = spatial_qc_workflow_viashalias.run(key: "spatial_qc_workflow")
|
||||
|
||||
// inner workflow
|
||||
|
||||
Reference in New Issue
Block a user