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add SigProfiler, SparseSignatures
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@Katerina10-cloud
Katerina10-cloud committed Jan 15, 2025
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Showing 1 changed file with 28 additions and 28 deletions.
56 changes: 28 additions & 28 deletions nextflow_schema.json
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"sparsesignatures_background_signature": {
"type": "string",
"default": "NULL",
"description": "A background signature provided by the user. The parameter is ignored if beta is given instead. If NULL, it is estimated through NMF."
"description": "A background signature provided by the user. The parameter is ignored if beta is given instead. If `NULL`, it is estimated through NMF."
},
"sparsesignatures_beta": {
"type": "string",
"default": "NULL",
"description": "The initial value of the signature matrix β. If NULL, it is estimated with a few runs of NMF. It must include the background signature as its first row."
"description": "The initial value of the signature matrix β. If `NULL`, it is estimated with a few runs of NMF. It must include the background signature as its first row."
},
"sparsesignatures_normalize_counts": {
"type": "string",
"default": "TRUE",
"description": "If TRUE normalize the count matrix x row-wise before processing it. Useful for algorithm stability, when considerably different total counts of mutations are observed among the patients."
"description": "If `TRUE` normalize the count matrix x row-wise before processing it. Useful for algorithm stability, when considerably different total counts of mutations are observed among the patients."
},
"sparsesignatures_iterations": {
"type": "integer",
Expand All @@ -494,7 +494,7 @@
"sparsesignatures_nmf_runs": {
"type": "integer",
"default": 10,
"description": "Number of iterations to estimate the length(K) matrices beta (including the background signature) in case the argument beta is NULL. Ignored if beta is given."
"description": "Number of iterations to estimate the length(K) matrices beta (including the background signature) in case the argument beta is `NULL`. Ignored if beta is given."
},
"sparsesignatures_max_iterations_lasso": {
"type": "integer",
Expand All @@ -504,7 +504,7 @@
"sparsesignatures_num_processes": {
"type": "string",
"default": "all",
"description": "The number of requested NMF worker subprocesses to spawn. If all, an adaptive maximum number is automatically chosen. If NA or NULL, the function is run by the main R session as a single process."
"description": "The number of requested NMF worker subprocesses to spawn. If all, an adaptive maximum number is automatically chosen. If `NA` or `NULL`, the function is run by the main R session as a single process."
},
"sparsesignatures_cross_validation_entries": {
"type": "number",
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"sparsesignatures_verbose": {
"type": "string",
"default": "TRUE",
"description": "If TRUE, print completion-status and descriptive messages over the function run."
"description": "If `TRUE`, print completion-status and descriptive messages over the function run."
},
"sparsesignatures_seed": {
"type": "integer",
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"download_sigprofiler_genome": {
"type": "boolean",
"default": true,
"description": "Specify if download SigProfiler reference genome, default value is true. Othervise, provide the path to the installed genome"
"description": "Specify if download SigProfiler reference genome, default value is `true`. Othervise, provide the path to the installed genome."
},
"genome_installed_path": {
"type": "string",
"description" : "The path to SigProfilerMatrixGenerator installed genome, where reference genomes will be loaded from, e.g. /path/to/directory/signature_deconvolution/SigProfiler/genome/tsb/"
"description" : "The path to SigProfilerMatrixGenerator installed genome, where reference genomes will be loaded from, e.g. `/path/to/directory/signature_deconvolution/SigProfiler/genome/tsb/`."
},
"sigprofiler_exome": {
"type": "string",
Expand All @@ -582,12 +582,12 @@
"sigprofiler_minimum_signatures": {
"type": "integer",
"default": 1,
"description": "The minimum number of signatures to be extracted"
"description": "The minimum number of signatures to be extracted."
},
"sigprofiler_maximum_signatures": {
"type": "integer",
"default": 25,
"description": "The maximum number of signatures to be extracted"
"description": "The maximum number of signatures to be extracted."
},
"sigprofiler_context_type": {
"type": "string",
Expand All @@ -597,42 +597,42 @@
"sigprofiler_nmf_replicates": {
"type": "integer",
"default": 100,
"description": "The number of iteration to be performed to extract each number signature"
"description": "The number of iteration to be performed to extract each number signature."
},
"sigprofiler_resample": {
"type": "string",
"default": "True",
"description": "If True, add poisson noise to samples by resampling"
"description": "If `True`, add poisson noise to samples by resampling."
},
"sigprofiler_matrix_normalization": {
"type": "string",
"default": "gmm",
"description": "Method of normalizing the genome matrix before it is analyzed by NMF. Options are, 'log2', 'custom' or 'none'."
"description": "Method of normalizing the genome matrix before it is analyzed by NMF. Options are, `log2`, `custom` or `none`."
},
"sigprofiler_nmf_init": {
"type": "string",
"default": "random",
"description": "The initialization algorithm for W and H matrix of NMF. Options are 'random', 'nndsvd', 'nndsvda', 'nndsvdar' and 'nndsvd_min'."
"description": "The initialization algorithm for W and H matrix of NMF. Options are `random`, `nndsvd`, `nndsvda`, `nndsvdar` and `nndsvd_min`."
},
"sigprofiler_min_nmf_iterations": {
"type": "integer",
"default": 10000,
"description": "Value defines the minimum number of iterations to be completed before NMF converges "
"description": "Value defines the minimum number of iterations to be completed before NMF converges."
},
"sigprofiler_max_nmf_iterations": {
"type": "integer",
"default": 1000000,
"description": "Value defines the maximum number of iterations to be completed before NMF converges"
"description": "Value defines the maximum number of iterations to be completed before NMF converges."
},
"sigprofiler_nmf_test_conv": {
"type": "integer",
"default": 10000,
"description": "Value defines the number number of iterations to done between checking next convergence"
"description": "Value defines the number number of iterations to done between checking next convergence."
},
"sigprofiler_seeds": {
"type": "string",
"default": "random",
"description": "Ensures reproducible NMF replicate resamples. Provide the path to the Seeds.txt file (found in the results folder from a previous analysis) to reproduce results"
"description": "Ensures reproducible NMF replicate resamples. Provide the path to the Seeds.txt file (found in the results folder from a previous analysis) to reproduce results."
},
"sigprofiler_stability": {
"type": "number",
Expand All @@ -657,12 +657,12 @@
"sigprofiler_make_decomposition_plots": {
"type": "string",
"default": "True",
"description": "Generate de novo to COSMIC signature decomposition plots as part of the results (default: True). Set to False to skip generating these plots."
"description": "Generate de novo to COSMIC signature decomposition plots as part of the results (default: `True`). Set to False to skip generating these plots."
},
"sigprofiler_collapse_to_SBS96": {
"type": "string",
"default": "True",
"description": "If True, SBS288 and SBS1536 de novo signatures will be mapped to SBS96 reference signatures (default: True). If False, those will be mapped to reference signatures of the same context."
"description": "If `True`, SBS288 and SBS1536 de novo signatures will be mapped to SBS96 reference signatures (default: `True`). If False, those will be mapped to reference signatures of the same context."
},
"sigprofiler_cosmic_version": {
"type": "number",
Expand All @@ -677,12 +677,12 @@
"sigprofiler_export_probabilities": {
"type": "string",
"default": "True",
"description": "Create the probability matrix"
"description": "Create the probability matrix."
},
"sigprofiler_chrom_based": {
"type": "string",
"default": "False",
"description": "Outputs chromosome-based matrices"
"description": "Outputs chromosome-based matrices."
},
"sigprofiler_bed_file": {
"type": "string",
Expand All @@ -692,7 +692,7 @@
"sigprofiler_plot": {
"type": "string",
"default": "False",
"description": "Integrates with SigProfilerPlotting to output all available visualizations for each matrix. "
"description": "Integrates with SigProfilerPlotting to output all available visualizations for each matrix."
},
"sigprofiler_seqInfo": {
"type": "string",
Expand All @@ -702,17 +702,17 @@
"sigprofiler_precision": {
"type": "string",
"default": "single",
"description": "Values should be single or double"
"description": "Values should be single or double."
},
"sigprofiler_cushion": {
"type": "integer",
"default": 100,
"description": "Adds an Xbp cushion to the exome/bed_file ranges for downsampling the mutations. "
"description": "Adds an Xbp cushion to the exome/bed_file ranges for downsampling the mutations."
},
"sigprofiler_gpu": {
"type": "string",
"default": "False",
"description": "Defines if the GPU resource will used if available (default: False). If True, the GPU resources will be used in the computation. Note: All available CPU processors are used by default, which may cause a memory error. This error can be resolved by reducing the number of CPU processes through the cpu parameter."
"description": "Defines if the GPU resource will used if available (default: `False`). If `True`, the GPU resources will be used in the computation. Note: All available CPU processors are used by default, which may cause a memory error. This error can be resolved by reducing the number of CPU processes through the cpu parameter."
},
"sigprofiler_tsb_stat": {
"type": "string",
Expand All @@ -727,12 +727,12 @@
"sigprofiler_allow_stability_drop": {
"type": "string",
"default": "False",
"description": "Defines if solutions with a drop in stability with respect to the highest stable number of signatures will be considered"
"description": "Defines if solutions with a drop in stability with respect to the highest stable number of signatures will be considered."
},
"sigprofiler_nmf_tolerance": {
"type": "number",
"default": 1e-15,
"description": "Value defines the tolerance to achieve to converge "
"description": "Value defines the tolerance to achieve to converge."
}
},
"fa_icon": "fas fa-briefcase"
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