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params.config
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params.config
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params {
dir = '/data/TEST'
species_of_interest = 'Arabidopsis_thaliana'
species_of_interest_panther_HMM_for_gene_names_url = 'http://data.pantherdb.org/ftp/sequence_classifications/17.0/PANTHER_Sequence_Classification_files/PTHR17.0_arabidopsis'
panther_hmm_database_location = 'http://data.pantherdb.org/ftp/panther_library/17.0/PANTHER17.0_hmmscoring.tgz' // Use this if you wish to download the entire database which will take a significant amount of time because of its size
// panther_hmm_database_location = '/some/path/to/your/pre-downloaded/and/unzipped/PANTHER/database/folder/' // Use this if you hve already downloaded and unzipped the PANTHER database
panther_hmm_classifications_location = 'http://data.pantherdb.org/ftp/hmm_classifications/17.0/PANTHER17.0_HMM_classifications'
urls = "${projectDir}/../config/urls.txt"
dates = "${projectDir}/../config/dates.txt"
comparisons_4DTv = "${projectDir}/../config/comparisons_4DTv.txt"
venn_species_max_5 = "${projectDir}/../config/venn_species_max_5.txt"
genes = "${projectDir}/../config/genes.txt"
cafe5_n_gamma_cats = 1 // If 1 then use the base model; else use the gamma model with <cafe5_n_gamma_cats> gamma categories to test
cafe5_pvalue = 0.01
go_term_enrich_genome_id = 3702 // Arabidopsis_thaliana
go_term_enrich_annotation_id = "GO:0008150"
go_term_enrich_test = "FISHER"
go_term_enrich_correction = "FDR"
go_term_enrich_ngenes_per_test = 100
go_term_enrich_ntests = 5
}
includeConfig 'process.config'