Build branch fix-integration-tests with version dev (2dbe3b72)
Build pipeline: vsh-ci-dev-k8tz4
Source commit: 2dbe3b7231
Source message: Fix pointers to test resources
This commit is contained in:
367
target/executable/annotate/onclass/.config.vsh.yaml
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367
target/executable/annotate/onclass/.config.vsh.yaml
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name: "onclass"
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namespace: "annotate"
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version: "dev"
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authors:
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- name: "Jakub Majercik"
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roles:
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- "author"
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info:
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role: "Contributor"
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links:
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email: "jakub@data-intuitive.com"
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github: "jakubmajercik"
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linkedin: "jakubmajercik"
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organizations:
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- name: "Data Intuitive"
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href: "https://www.data-intuitive.com"
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role: "Bioinformatics Engineer"
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argument_groups:
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- name: "Inputs"
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description: "Input dataset (query) arguments"
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arguments:
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- type: "file"
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name: "--input"
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alternatives:
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- "-i"
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description: "The input (query) data to be labeled. Should be a .h5mu file."
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info: null
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example:
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- "input.h5mu"
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--modality"
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description: "Which modality to process."
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info: null
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default:
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- "rna"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--input_layer"
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description: "The layer in the input data to be used for cell type annotation\
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\ if .X is not to be used."
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--cl_nlp_emb_file"
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description: "The .nlp.emb file with the cell type embeddings."
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info: null
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--cl_ontology_file"
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description: "The .ontology file with the cell type ontology."
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info: null
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--cl_obo_file"
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description: "The .obo file with the cell type ontology."
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info: null
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--var_query_gene_names"
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description: "The name of the adata var column in the input data containing gene\
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\ names; when no gene_name_layer is provided, the var index will be used.\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Reference"
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description: "Arguments related to the reference dataset."
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arguments:
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- type: "file"
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name: "--reference"
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description: "The reference data to train the CellTypist classifiers on. Only\
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\ required if a pre-trained --model is not provided."
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info: null
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example:
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- "reference.h5mu"
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must_exist: true
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create_parent: true
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--reference_layer"
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description: "The layer in the reference data to be used for cell type annotation\
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\ if .X is not to be used."
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--reference_obs_target"
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description: "The name of the adata obs column in the reference data containing\
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\ cell type annotations."
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info: null
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example:
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- "cell_ontology_class"
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Outputs"
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description: "Output arguments."
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arguments:
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- type: "file"
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name: "--output"
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description: "Output h5mu file."
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info: null
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example:
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- "output.h5mu"
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must_exist: true
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create_parent: true
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required: false
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--output_compression"
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info: null
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example:
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- "gzip"
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required: false
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choices:
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- "gzip"
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- "lzf"
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--output_obs_predictions"
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description: "In which `.obs` slots to store the predicted information.\n"
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info: null
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default:
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- "onclass_pred"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--output_obs_probability"
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description: "In which `.obs` slots to store the probability of the predictions.\n"
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info: null
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default:
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- "onclass_prob"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Model arguments"
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description: "Model arguments"
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arguments:
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- type: "string"
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name: "--model"
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description: "\"Pretrained model path without a file extension. If not provided,\
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\ the model will be trained \non the reference data and --reference should be\
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\ provided. The path namespace should contain:\n - a .npz or .pkl file\n -\
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\ a .data file\n - a .meta file\n - a .index file\ne.g. /path/to/model/pretrained_model_target1\
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\ as saved by OnClass.\"\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "integer"
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name: "--max_iter"
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description: "Maximum number of iterations for training the model."
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info: null
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default:
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- 30
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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resources:
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- type: "python_script"
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path: "script.py"
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is_executable: true
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- type: "file"
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path: "setup_logger.py"
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- type: "file"
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path: "nextflow_labels.config"
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dest: "nextflow_labels.config"
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description: "OnClass is a python package for single-cell cell type annotation. It\
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\ uses the Cell Ontology to capture the cell type similarity. \nThese similarities\
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\ enable OnClass to annotate cell types that are never seen in the training data.\n"
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test_resources:
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- type: "python_script"
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path: "test.py"
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is_executable: true
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- type: "file"
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path: "annotation_test_data"
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- type: "file"
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path: "pbmc_1k_protein_v3"
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- type: "file"
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path: "openpipelinetestutils"
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dest: "openpipelinetestutils"
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info: null
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status: "enabled"
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links:
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repository: "https://github.com/openpipelines-bio/openpipeline"
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docker_registry: "ghcr.io"
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runners:
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- type: "executable"
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id: "executable"
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docker_setup_strategy: "ifneedbepullelsecachedbuild"
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- type: "nextflow"
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id: "nextflow"
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directives:
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tag: "$id"
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auto:
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simplifyInput: true
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simplifyOutput: false
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transcript: false
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publish: false
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config:
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labels:
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mem1gb: "memory = 1000000000.B"
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mem2gb: "memory = 2000000000.B"
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mem5gb: "memory = 5000000000.B"
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mem10gb: "memory = 10000000000.B"
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mem20gb: "memory = 20000000000.B"
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mem50gb: "memory = 50000000000.B"
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mem100gb: "memory = 100000000000.B"
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mem200gb: "memory = 200000000000.B"
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mem500gb: "memory = 500000000000.B"
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mem1tb: "memory = 1000000000000.B"
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mem2tb: "memory = 2000000000000.B"
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mem5tb: "memory = 5000000000000.B"
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mem10tb: "memory = 10000000000000.B"
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mem20tb: "memory = 20000000000000.B"
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mem50tb: "memory = 50000000000000.B"
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mem100tb: "memory = 100000000000000.B"
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mem200tb: "memory = 200000000000000.B"
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mem500tb: "memory = 500000000000000.B"
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mem1gib: "memory = 1073741824.B"
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mem2gib: "memory = 2147483648.B"
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mem4gib: "memory = 4294967296.B"
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mem8gib: "memory = 8589934592.B"
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mem16gib: "memory = 17179869184.B"
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mem32gib: "memory = 34359738368.B"
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mem64gib: "memory = 68719476736.B"
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mem128gib: "memory = 137438953472.B"
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mem256gib: "memory = 274877906944.B"
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mem512gib: "memory = 549755813888.B"
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mem1tib: "memory = 1099511627776.B"
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mem2tib: "memory = 2199023255552.B"
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mem4tib: "memory = 4398046511104.B"
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mem8tib: "memory = 8796093022208.B"
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mem16tib: "memory = 17592186044416.B"
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mem32tib: "memory = 35184372088832.B"
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mem64tib: "memory = 70368744177664.B"
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mem128tib: "memory = 140737488355328.B"
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mem256tib: "memory = 281474976710656.B"
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mem512tib: "memory = 562949953421312.B"
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cpu1: "cpus = 1"
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cpu2: "cpus = 2"
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cpu5: "cpus = 5"
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cpu10: "cpus = 10"
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cpu20: "cpus = 20"
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cpu50: "cpus = 50"
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cpu100: "cpus = 100"
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cpu200: "cpus = 200"
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cpu500: "cpus = 500"
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cpu1000: "cpus = 1000"
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script:
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- "includeConfig(\"nextflow_labels.config\")"
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debug: false
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container: "docker"
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engines:
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- type: "docker"
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id: "docker"
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image: "python:3.8"
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target_registry: "images.viash-hub.com"
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target_tag: "dev"
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namespace_separator: "/"
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setup:
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- type: "python"
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user: false
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packages:
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- "scikit-learn==0.24.0"
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- "OnClass==1.2"
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- "tensorflow==2.13.1"
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- "obonet==1.1.0"
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- "mudata"
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upgrade: true
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test_setup:
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- type: "docker"
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copy:
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- "openpipelinetestutils /opt/openpipelinetestutils"
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- type: "python"
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user: false
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packages:
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- "/opt/openpipelinetestutils"
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upgrade: true
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- type: "python"
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user: false
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packages:
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- "viashpy==0.8.0"
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upgrade: true
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entrypoint: []
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cmd: null
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- type: "native"
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id: "native"
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build_info:
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config: "src/annotate/onclass/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/annotate/onclass"
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executable: "target/executable/annotate/onclass/onclass"
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viash_version: "0.9.0"
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git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
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git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
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git_tag: "0.2.0-1926-g2dbe3b72"
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package_config:
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name: "openpipeline"
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version: "dev"
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info:
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test_resources:
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- type: "s3"
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path: "s3://openpipelines-data"
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dest: "resources_test"
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viash_version: "0.9.0"
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source: "src"
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target: "target"
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config_mods:
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- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
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.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
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.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
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\ := 'includeConfig(\"nextflow_labels.config\")'"
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- ".engines += { type: \"native\" }"
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- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
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- ".engines[.type == 'docker'].target_tag := 'dev'"
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organization: "vsh"
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links:
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repository: "https://github.com/openpipelines-bio/openpipeline"
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docker_registry: "ghcr.io"
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homepage: "https://openpipelines.bio"
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documentation: "https://openpipelines.bio/fundamentals"
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issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
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42
target/executable/annotate/onclass/nextflow_labels.config
Normal file
42
target/executable/annotate/onclass/nextflow_labels.config
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@@ -0,0 +1,42 @@
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process {
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// Default resources for components that hardly do any processing
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memory = { 2.GB * task.attempt }
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cpus = 1
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// Retry for exit codes that have something to do with memory issues
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errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
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maxRetries = 3
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maxMemory = null
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// Resource labels
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withLabel: singlecpu { cpus = 1 }
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withLabel: lowcpu { cpus = 4 }
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withLabel: midcpu { cpus = 10 }
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withLabel: highcpu { cpus = 20 }
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withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
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withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
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withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
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withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
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}
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def get_memory(to_compare) {
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if (!process.containsKey("maxMemory") || !process.maxMemory) {
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return to_compare
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}
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try {
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if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
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return process.maxMemory
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}
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else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
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return max_memory as nextflow.util.MemoryUnit
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}
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else {
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return to_compare
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}
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} catch (all) {
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println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
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System.exit(1)
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}
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}
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1613
target/executable/annotate/onclass/onclass
Executable file
1613
target/executable/annotate/onclass/onclass
Executable file
File diff suppressed because it is too large
Load Diff
12
target/executable/annotate/onclass/setup_logger.py
Normal file
12
target/executable/annotate/onclass/setup_logger.py
Normal file
@@ -0,0 +1,12 @@
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def setup_logger():
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import logging
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from sys import stdout
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logger = logging.getLogger()
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logger.setLevel(logging.INFO)
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console_handler = logging.StreamHandler(stdout)
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logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
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console_handler.setFormatter(logFormatter)
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logger.addHandler(console_handler)
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return logger
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