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add missing files (schema, .nftignore) to repo
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‎nextflow_schema.json‎

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://raw.githubusercontent.com/dessimozlab/FastOMA/main/nextflow_schema.json",
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"title": "FastOMA Pipeline Parameters",
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"description": "Fast orthologous matrix analysis pipeline",
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"type": "object",
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"$defs": {
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"input_options": {
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"title": "Input options",
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"type": "object",
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"description": "Define where the pipeline should find input data ",
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"required": ["input_folder", "species_tree"],
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"properties": {
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"input_folder": {
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"type": "string",
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"format": "directory-path",
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"description": "Path to input directory containing proteomes and species tree",
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"fa_icon": "fas fa-folder-open"
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},
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"proteome_folder": {
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"type": "string",
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"format": "directory-path",
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"description": "Path to input directory containing the proteome files in fasta format",
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"help": "If not provided, the proteomes are asumed to be in the input_folder/proteomes directory.",
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"fa_icon": "fas fa-folder-open"
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},
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"hogmap_in": {
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"type": "string",
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"format": "directory-path",
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"description": "Path to input directory containing the hogmap files",
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"fa_icon": "fas fa-folder-open",
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"help": "If provided, the hogmap files will be used instead of computing them from scratch with OMAmer. This can save time if you have already computed the hogmaps for your proteomes."
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},
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"species_tree": {
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"type": "string",
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"format": "file-path",
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"description": "Path to species tree file",
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"fa_icon": "fas fa-tree",
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"pattern": "^\\S+\\.(nhx|nh|nwk)",
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"help": "The species tree should be in Newick or NHX format. By default, the pipeline looks for a file named species_tree.nwk in the input_folder."
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},
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"splice_folder": {
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"type": "string",
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"format": "directory-path",
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"description": "Path to input directory containing the splice files",
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"fa_icon": "fas fa-folder-open",
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"help": "If provided, FastOMA will use the splice files to identify and handle alternative splicing isoforms in the proteomes and select the best representative isoform for each gene."
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},
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"omamer_db": {
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"type": "string",
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"format": "file-path",
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"description": "Path to OMAmer database against which the proteomes will be mapped",
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"fa_icon": "fas fa-database",
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"help": "If not provided, the default OMAmer database (LUCA) will be used.",
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"default": "https://omabrowser.org/All/LUCA.h5"
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}
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}
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},
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"output_options": {
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"title": "Output options",
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"type": "object",
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"description": "Define where the pipeline should store the output data",
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"required": ["output_folder"],
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"properties": {
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"output_folder": {
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"type": "string",
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"default": "Output",
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"format": "directory-path",
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"description": "The output directory where the results will be saved",
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"fa_icon": "fas fa-folder-open"
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},
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"hogmap_folder": {
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"type": "string",
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"format": "directory-path",
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"description": "The output directory where the omamer hogmap files will be saved",
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"help": "If not provided, the hogmap files will be saved in the output_folder/hogmap directory.",
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"fa_icon": "fas fa-folder-open",
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"default": "Output/hogmap"
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}
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}
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},
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"processing_options": {
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"title": "Processing options",
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"type": "object",
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"description": "Parameters for processing and analysis",
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"properties": {
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"fasta_header_id_transformer": {
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"type": "string",
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"default": "noop",
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"enum": ["noop", "UniProt"],
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"description": "FASTA header ID transformer method"
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},
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"filter_method": {
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"type": "string",
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"default": "col-row-threshold",
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"description": "MSA filtering method",
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"enum": ["col-row-threshold", "col-elbow-row-threshold", "trimal"]
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},
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"filter_gap_ratio_row": {
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"type": "number",
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"default": 0.3,
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"minimum": 0,
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"maximum": 1,
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"description": "Gap ratio threshold for row filtering"
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},
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"filter_gap_ratio_col": {
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"type": "number",
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"default": 0.5,
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"minimum": 0,
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"maximum": 1
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},
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"nr_repr_per_hog": {
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"type": "integer",
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"default": 5,
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"minimum": 1
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},
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"min_sequence_length": {
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"type": "integer",
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"default": 20
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}
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}
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},
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"output_control": {
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"title": "Output control",
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"type": "object",
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"description": "Control what outputs are saved",
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"properties": {
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"write_msas": {
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"type": "boolean",
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"description": "Write multiple sequence alignments"
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},
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"write_genetrees": {
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"type": "boolean",
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"description": "Write gene trees"
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},
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"debug_enabled": {
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"type": "boolean",
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"description": "Enable debug mode"
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},
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"msa_folder": {
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"type": "string",
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"default": "Output/msa"
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},
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"temp_output": {
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"type": "string",
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"default": "Output/temp_output"
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},
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"genetrees_folder": {
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"type": "string",
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"default": "Output/genetrees"
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},
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"force_pairwise_ortholog_generation": {
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"type": "boolean",
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"description": "Force generation of pairwise orthologs even for large datasets (may be slow)",
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"help": "By default, pairwise orthologs are not generated for datasets with more than 25 species to avoid long runtimes. Enable this option to override this behavior."
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}
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}
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},
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"resource_options": {
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"title": "Resource options",
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"type": "object",
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"description": "",
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"default": "",
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"properties": {
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"time_multiplier": {
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"type": "integer",
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"default": 1
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},
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"memory_multiplier": {
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"type": "integer",
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"default": 1
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}
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}
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},
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"generic_options": {
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"title": "Generic options",
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"type": "object",
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"description": "Less common options for the pipeline",
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"properties": {
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"help": {
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"type": "boolean",
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"description": "Display help text",
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"fa_icon": "fas fa-question-circle",
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"hidden": true
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},
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"report": {
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"type": "boolean",
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"description": "Generate nextflow reports"
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},
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"statsdir": {
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"type": "string",
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"fa_icon": "fas fa-folder-open",
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"default": "Output/stats"
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},
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"trace_report_suffix": {
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"type": "string",
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"fa_icon": "far calendar",
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"description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
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"hidden": true
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},
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"custom_config_version": {
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"type": "string",
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"default": "master"
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},
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"custom_config_base": {
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"type": "string",
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"default": "https://raw.githubusercontent.com/nf-core/configs/master"
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},
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"container_name": {
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"type": "string",
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"default": "dessimozlab/fastoma"
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},
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"container_version": {
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"type": "string",
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"default": "dev"
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/$defs/input_options"
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},
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{
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"$ref": "#/$defs/output_options"
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},
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{
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"$ref": "#/$defs/processing_options"
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},
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{
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"$ref": "#/$defs/output_control"
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},
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{
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"$ref": "#/$defs/resource_options"
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},
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{
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"$ref": "#/$defs/generic_options"
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}
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]
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}

‎nf-test.config‎

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config {
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// location for all nf-tests
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testsDir "nf-tests/"
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testsDir "./"
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// nf-test directory including temporary files for each test
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workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"

‎nf-tests/.nftignore‎

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.DS_Store
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RootHOGs.tsv
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OrthologousGroups.tsv
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FastOMA_HOGs.orthoxml
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orthologs.tsv.gz
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report.*
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**/*.html
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**/*.hogmap

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