From eff2e81713a13b273ea51b51c75baed6a23be422 Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 10:38:04 +0200 Subject: [PATCH 01/15] add propr, mygene and fiter_var module --- modules/local/filtervar/main.nf | 23 + modules/local/filtervar/templates/filtervar.R | 275 +++++++++++ modules/nf-core/mygene/environment.yml | 7 + modules/nf-core/mygene/main.nf | 23 + modules/nf-core/mygene/meta.yml | 54 +++ modules/nf-core/mygene/templates/mygene.py | 307 ++++++++++++ .../nf-core/mygene/tests/default_tsv.config | 3 + .../nf-core/mygene/tests/go_category.config | 3 + .../nf-core/mygene/tests/go_evidence.config | 3 + modules/nf-core/mygene/tests/main.nf.test | 106 ++++ .../nf-core/mygene/tests/main.nf.test.snap | 135 ++++++ modules/nf-core/mygene/tests/tags.yml | 2 + modules/nf-core/propr/grea/environment.yml | 7 + modules/nf-core/propr/grea/main.nf | 24 + modules/nf-core/propr/grea/meta.yml | 57 +++ modules/nf-core/propr/grea/templates/grea.R | 253 ++++++++++ .../nf-core/propr/grea/tests/grea_test.config | 8 + modules/nf-core/propr/grea/tests/main.nf.test | 62 +++ .../propr/grea/tests/main.nf.test.snap | 31 ++ modules/nf-core/propr/grea/tests/tags.yml | 2 + modules/nf-core/propr/propd/environment.yml | 7 + modules/nf-core/propr/propd/main.nf | 28 ++ modules/nf-core/propr/propd/meta.yml | 68 +++ modules/nf-core/propr/propd/templates/propd.R | 372 ++++++++++++++ .../propr/propd/tests/adjacency.config | 3 + .../propr/propd/tests/boxcox_theta_e.config | 4 + .../propr/propd/tests/default_boxcox.config | 4 + .../propd/tests/default_permutation.config | 4 + .../nf-core/propr/propd/tests/main.nf.test | 154 ++++++ .../propr/propd/tests/main.nf.test.snap | 133 ++++++ modules/nf-core/propr/propd/tests/tags.yml | 2 + .../nf-core/propr/propd/tests/theta_e.config | 4 + modules/nf-core/propr/propr/environment.yml | 7 + modules/nf-core/propr/propr/main.nf | 27 ++ modules/nf-core/propr/propr/meta.yml | 76 +++ modules/nf-core/propr/propr/templates/propr.R | 452 ++++++++++++++++++ .../propr/propr/tests/adjacency.config | 3 + .../propr/propr/tests/adjacency_pcor.config | 3 + .../propr/propr/tests/adjacency_phs.config | 3 + .../propr/propr/tests/adjacency_rho.config | 3 + .../propr/propr/tests/alr_pcorbshrink.config | 3 + .../nf-core/propr/propr/tests/clr_pcor.config | 3 + .../propr/propr/tests/clr_pcorbshrink.config | 3 + .../nf-core/propr/propr/tests/clr_rho.config | 3 + .../propr/propr/tests/clr_rho_alpha.config | 3 + .../nf-core/propr/propr/tests/main.nf.test | 240 ++++++++++ .../propr/propr/tests/main.nf.test.snap | 354 ++++++++++++++ modules/nf-core/propr/propr/tests/tags.yml | 2 + 48 files changed, 3353 insertions(+) create mode 100644 modules/local/filtervar/main.nf create mode 100644 modules/local/filtervar/templates/filtervar.R create mode 100644 modules/nf-core/mygene/environment.yml create mode 100644 modules/nf-core/mygene/main.nf create mode 100644 modules/nf-core/mygene/meta.yml create mode 100644 modules/nf-core/mygene/templates/mygene.py create mode 100644 modules/nf-core/mygene/tests/default_tsv.config create mode 100644 modules/nf-core/mygene/tests/go_category.config create mode 100644 modules/nf-core/mygene/tests/go_evidence.config create mode 100644 modules/nf-core/mygene/tests/main.nf.test create mode 100644 modules/nf-core/mygene/tests/main.nf.test.snap create mode 100644 modules/nf-core/mygene/tests/tags.yml create mode 100644 modules/nf-core/propr/grea/environment.yml create mode 100644 modules/nf-core/propr/grea/main.nf create mode 100644 modules/nf-core/propr/grea/meta.yml create mode 100644 modules/nf-core/propr/grea/templates/grea.R create mode 100644 modules/nf-core/propr/grea/tests/grea_test.config create mode 100644 modules/nf-core/propr/grea/tests/main.nf.test create mode 100644 modules/nf-core/propr/grea/tests/main.nf.test.snap create mode 100644 modules/nf-core/propr/grea/tests/tags.yml create mode 100644 modules/nf-core/propr/propd/environment.yml create mode 100644 modules/nf-core/propr/propd/main.nf create mode 100644 modules/nf-core/propr/propd/meta.yml create mode 100644 modules/nf-core/propr/propd/templates/propd.R create mode 100644 modules/nf-core/propr/propd/tests/adjacency.config create mode 100755 modules/nf-core/propr/propd/tests/boxcox_theta_e.config create mode 100755 modules/nf-core/propr/propd/tests/default_boxcox.config create mode 100755 modules/nf-core/propr/propd/tests/default_permutation.config create mode 100755 modules/nf-core/propr/propd/tests/main.nf.test create mode 100644 modules/nf-core/propr/propd/tests/main.nf.test.snap create mode 100755 modules/nf-core/propr/propd/tests/tags.yml create mode 100755 modules/nf-core/propr/propd/tests/theta_e.config create mode 100644 modules/nf-core/propr/propr/environment.yml create mode 100644 modules/nf-core/propr/propr/main.nf create mode 100644 modules/nf-core/propr/propr/meta.yml create mode 100644 modules/nf-core/propr/propr/templates/propr.R create mode 100644 modules/nf-core/propr/propr/tests/adjacency.config create mode 100644 modules/nf-core/propr/propr/tests/adjacency_pcor.config create mode 100644 modules/nf-core/propr/propr/tests/adjacency_phs.config create mode 100644 modules/nf-core/propr/propr/tests/adjacency_rho.config create mode 100644 modules/nf-core/propr/propr/tests/alr_pcorbshrink.config create mode 100644 modules/nf-core/propr/propr/tests/clr_pcor.config create mode 100644 modules/nf-core/propr/propr/tests/clr_pcorbshrink.config create mode 100644 modules/nf-core/propr/propr/tests/clr_rho.config create mode 100644 modules/nf-core/propr/propr/tests/clr_rho_alpha.config create mode 100644 modules/nf-core/propr/propr/tests/main.nf.test create mode 100644 modules/nf-core/propr/propr/tests/main.nf.test.snap create mode 100644 modules/nf-core/propr/propr/tests/tags.yml diff --git a/modules/local/filtervar/main.nf b/modules/local/filtervar/main.nf new file mode 100644 index 00000000..bf8e3ae2 --- /dev/null +++ b/modules/local/filtervar/main.nf @@ -0,0 +1,23 @@ +process FILTERVAR { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/r-propr:5.0.3': + 'quay.io/biocontainers/r-propr:5.0.3' }" + + input: + tuple val(meta), path(count), path(adj_matrix) + + output: + tuple val(meta), path("*.count_filtered.tsv"), emit: count + path "*.R_sessionInfo.log", emit: session_info + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'filtervar.R' +} \ No newline at end of file diff --git a/modules/local/filtervar/templates/filtervar.R b/modules/local/filtervar/templates/filtervar.R new file mode 100644 index 00000000..cf5159c9 --- /dev/null +++ b/modules/local/filtervar/templates/filtervar.R @@ -0,0 +1,275 @@ + + +#!/usr/bin/env Rscript + + +################################################ +################################################ +## Functions ## +################################################ +################################################ + +#' Parse out options from a string without recourse to optparse +#' +#' @param x Long-form argument list like --opt1 val1 --opt2 val2 +#' +#' @return named list of options and values similar to optparse + +parse_args <- function(x){ + args_list <- unlist(strsplit(x, ' ?--')[[1]])[-1] + args_vals <- lapply(args_list, function(x) scan(text=x, what='character', quiet = TRUE)) + + # Ensure the option vectors are length 2 (key/ value) to catch empty ones + args_vals <- lapply(args_vals, function(z){ length(z) <- 2; z}) + + parsed_args <- structure(lapply(args_vals, function(x) x[2]), names = lapply(args_vals, function(x) x[1])) + parsed_args[! is.na(parsed_args)] +} + +#' Flexibly read CSV or TSV files +#' +#' @param file Input file +#' @param header Boolean. TRUE if first row is header. False without header. +#' @param row.names The first column is used as row names by default. +#' Otherwise, give another number. Or use NULL when no row.names are present. +#' +#' @return output Data frame +read_delim_flexible <- function(file, header = TRUE, row.names = 1, check.names = TRUE){ + + ext <- tolower(tail(strsplit(basename(file), split = "\\\\.")[[1]], 1)) + + if (ext == "tsv" || ext == "txt") { + separator <- "\\t" + } else if (ext == "csv") { + separator <- "," + } else { + stop(paste("Unknown separator for", ext)) + } + + mat <- read.delim( + file, + sep = separator, + header = header, + row.names = row.names, + check.names = check.names + ) + + if ( (row.names == 'gene_id') & ('gene_name' %in% colnames(mat)) ){ + mat <- mat[, -which(colnames(mat) == 'gene_name')] + } else if ( (row.names == 'gene_name') & ('gene_id' %in% colnames(mat)) ){ + mat <- mat[, -which(colnames(mat) == 'gene_id')] + } + + return(mat) +} + +read_delim_flexible2 <- function(file, header = TRUE){ + + ext <- tolower(tail(strsplit(basename(file), split = "\\\\.")[[1]], 1)) + + if (ext == "tsv" || ext == "txt") { + separator <- "\\t" + } else if (ext == "csv") { + separator <- "," + } else { + stop(paste("Unknown separator for", ext)) + } + + mat <- read.delim( + file, + sep = separator, + header = header + ) + return(mat) +} + + + +################################################ +################################################ +## Parse arguments ## +################################################ +################################################ + +opt <- list( + count = '$count', + prefix = ifelse('$task.ext.prefix' == 'null', '$meta.pathway_name', '$task.ext.prefix'), + transformation = 'clr', + reference = NA, + alpha = NA, + metric = 'pcor.bshrink', + permutation = 0, + cutoff_min = NA, + cutoff_max = NA, + cutoff_interval = NA, + ncores = as.integer('$task.cpus'), + features_id_col = 'gene_id', + fixseed = FALSE, + adjacency = FALSE, + fdrVal = 0.05, + adj_matrix = '$adj_matrix', + filterVar = 'yes' +) +opt_types <- list( + count = 'character', + prefix = 'character', + transformation = 'character', + reference = 'character', + alpha = 'numeric', + metric = 'character', + permutation = 'numeric', + cutoff_min = 'numeric', + cutoff_max = 'numeric', + cutoff_interval = 'numeric', + ncores = 'numeric', + features_id_col = 'character', + fixseed = 'logical', + adjacency = 'logical', + fdrVal = 'numeric', + adj_matrix = 'character', + filterVar = 'character' +) + + +# Apply parameter overrides +args_opt <- parse_args('$task.ext.args') + +for ( ao in names(args_opt)){ + if (! ao %in% names(opt)){ + stop(paste("Invalid option:", ao)) + } else { + + # Preserve classes from defaults where possible + if (! is.null(opt[[ao]])){ + args_opt[[ao]] <- as(args_opt[[ao]], opt_types[[ao]]) + } + # set NA + if (args_opt[[ao]] %in% c('NA', NA, 'null')){ + args_opt[[ao]] <- NA + } + opt[[ao]] <- args_opt[[ao]] + } +} + +# Check if required parameters have been provided +required_opts <- c('count') +missing <- required_opts[unlist(lapply(opt[required_opts], is.null)) | ! required_opts %in% names(opt)] +if (length(missing) > 0){ + stop(paste("Missing required options:", paste(missing, collapse=', '))) +} + +################################################ +################################################ +## Perform variable selection ## +################################################ +################################################ + +# read matrix +A <- read_delim_flexible( + opt\$adj_matrix, + header = TRUE, + row.names = 1, + check.names = TRUE +) + +count <- read_delim_flexible2( + opt\$count, + header = TRUE +) + +### Determine most differentially proportional genes + +# Set diagonal in A to 0 +diag(A) <- 0 + +# Sum values in adjacency and add as an extra column +per_gene_connection <- rowSums(A) + +A\$per_gene <- per_gene_connection + +A <- A[order(A\$per_gene, decreasing = TRUE),] + +# Define selection criteria + +max_gene_number <- ncol(count)*10 # 10x samples for technical reasons (pcor) + +#Calculate connection threshold +total_connections <- sum(per_gene_connection)/2 # 2 because the matrix is symmetric +possible_connections <- nrow(count)*(nrow(count)-1)/2 + +percentage_expected <- total_connections/possible_connections +connection_threshold <- percentage_expected * nrow(count) + +# Filter count matrix according to selected genes + +col_genes <- which(names(count) == opt\$features_id_col) + +if (opt\$filterVar == 'yes'){ + # select only differentially proportional genes + top_genes <- rownames(A[which(A\$per_gene > connection_threshold),]) + count_filtered <- count[count[,col_genes] %in% top_genes,] + warning("non differentially proportional genes were removed before correlation analysis") + +} else if (max_gene_number < nrow(count) & opt\$metric== 'pcor.bshrink'){ + # select the maximum number of genes to perform partial correlation + top_genes <- rownames(A[1:gene_number,]) + count_filtered <- count[count[,col_genes] %in% top_genes,] + warning("some genes were removed to perform partial correlation") + +}else{ + # no genes were removed + count_filtered <- count + warning("No genes were removed") +} + + +################################################ +################################################ +## Generate outputs ## +################################################ +################################################ + +write.table( + count_filtered, + file = paste0(opt\$prefix, '.count_filtered.tsv'), + col.names = TRUE, + row.names = FALSE, + sep = '\t', + quote = FALSE +) + +################################################ +################################################ +## WARNINGS ## +################################################ +################################################ + +sink(paste0(opt\$prefix, ".warnings.log")) +print(warnings()) +sink() + +################################################ +################################################ +## R SESSION INFO ## +################################################ +################################################ + +sink(paste0(opt\$prefix, ".R_sessionInfo.log")) +print(sessionInfo()) +sink() + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +propr.version <- as.character(packageVersion('propr')) + +writeLines( + c( + '"${task.process}":', + paste(' r-propr:', propr.version) + ), +'versions.yml') + diff --git a/modules/nf-core/mygene/environment.yml b/modules/nf-core/mygene/environment.yml new file mode 100644 index 00000000..45442c49 --- /dev/null +++ b/modules/nf-core/mygene/environment.yml @@ -0,0 +1,7 @@ +name: mygene +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::mygene=3.2.2 diff --git a/modules/nf-core/mygene/main.nf b/modules/nf-core/mygene/main.nf new file mode 100644 index 00000000..27066b71 --- /dev/null +++ b/modules/nf-core/mygene/main.nf @@ -0,0 +1,23 @@ +process MYGENE { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mygene:3.2.2--pyh5e36f6f_0': + 'quay.io/biocontainers/mygene:3.2.2--pyh5e36f6f_0' }" + + input: + tuple val(meta), path(gene_list) + + output: + tuple val(meta), path("*.gmt"), emit: gmt + tuple val(meta), path("*.tsv"), emit: tsv , optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template "mygene.py" +} diff --git a/modules/nf-core/mygene/meta.yml b/modules/nf-core/mygene/meta.yml new file mode 100644 index 00000000..f7aaa455 --- /dev/null +++ b/modules/nf-core/mygene/meta.yml @@ -0,0 +1,54 @@ +name: "mygene" +description: Fetch the GO concepts for a list of genes +keywords: + - mygene + - go + - annotation +tools: + - "mygene": + description: "A python wrapper to query/retrieve gene annotation data from Mygene.info." + homepage: "https://mygene.info/" + documentation: "https://docs.mygene.info/projects/mygene-py/en/latest/" + tool_dev_url: "https://github.com/biothings/mygene.py" + doi: "10.1093/nar/gks1114" + licence: ["Apache-2.0"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - gene_list: + type: file + description: A tsv/csv file that contains a list of gene ids in one of the columns. + By default, the column name should be "gene_id", but this can be changed + by using "--columname gene_id" in ext.args. + pattern: "*.{csv,tsv}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - gmt: + type: file + description: | + Each row contains the GO id, a description, and a list of gene ids. + pattern: "*.gmt" + - tsv: + type: file + description: | + (optional) A tsv file with the following columns: + query, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid + pattern: "*.tsv" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@suzannejin" +maintainers: + - "@suzannejin" diff --git a/modules/nf-core/mygene/templates/mygene.py b/modules/nf-core/mygene/templates/mygene.py new file mode 100644 index 00000000..201977a0 --- /dev/null +++ b/modules/nf-core/mygene/templates/mygene.py @@ -0,0 +1,307 @@ +#!/usr/bin/env python3 +import argparse +import mygene +import shlex + + +""" +This python script uses the mygene module to query the MyGene.info API and +retrieve the go terms associated with a list of gene ids. The gene ids should +ideally be Ensembl or Entrez ids. The script generates two outputs: + 1. A tsv file containing information related to each query. The columns + include query, mygene_id, go_id, go_term, go_evidence, go_category, + symbol, name, and taxid. + 2. A gmt file containing information related to each go term. Each row + includes the go id, go term, and the genes associated with that go term. + +Author: Suzanne Jin +License: Apache 2.0 (same as the mygene library) +""" + + +class Arguments: + """ + Parses the argments, including the ones coming from $task.ext.args. + """ + def __init__(self) -> None: + self.input = "$gene_list" + self.prefix = ( + "$task.ext.prefix" + if "$task.ext.prefix" != "null" + else "$meta.id" + ) + self.output_gmt = self.prefix + ".gmt" + self.output_tsv = self.prefix + ".tsv" + self.parse_ext_args("$task.ext.args") + + def parse_ext_args(self, args_string: str) -> None: + """ + It parses the extended arguments. + """ + # skip when there are no extended arguments + if args_string == "null": + args_string = "" + + # Parse the extended arguments + args_list = shlex.split(args_string) # Split the string into a list of arguments + parser = argparse.ArgumentParser() + # input parameters + parser.add_argument('--columname', default='"gene_id"', help='Name of the column where the gene ids are stored in the input file. Default: gene_id') + # filtering parameters + parser.add_argument('--species', default=None, help="Comma separated of common name of the species or taxon ids") + parser.add_argument('--go_category', default=None, help="Comma separated list of GO categories to keep. Default: all") + parser.add_argument('--go_evidence', default=None, help="Comma separated list of GO evidence codes to keep. Default: all") + # additional parameters for querymany + parser.add_argument('--scopes', default=None, help="Comma separated list of scopes to search for.") + parser.add_argument('--entrezonly', default=False, help="When true, the query returns only the hits with valid Entrez gene ids. Default: false.") + parser.add_argument('--ensemblonly', default=False, help="When true, the query returns only the hits with valid Ensembl gene ids. Default: False") + # output parameters + parser.add_argument('--generate_tsv', default=False, help="Also generate a tsv file with the gene based information. Default: False") + args = parser.parse_args(args_list) + + # Convert "null" values to default values + # convert true to True and false to False + for attr in vars(args): + value = getattr(args, attr) + if value == "null": + setattr(args, attr, parser.get_default(attr)) + elif value == "true": + setattr(args, attr, True) + elif value == "false": + setattr(args, attr, False) + + # check if the arguments are valid + if args.go_category: + args.go_category = args.go_category.upper() + for category in args.go_category.split(","): + if category not in ["BP", "MF", "CC"]: + raise ValueError("The GO category should be one of BP, MF, or CC.") + if args.go_evidence: + args.go_evidence = args.go_evidence.upper() + + # Assign args attributes to self attributes + for attr in vars(args): + setattr(self, attr, getattr(args, attr)) + + def print_args(self) -> None: + """ + Print the arguments. + """ + for attr in vars(self): + print(f"{attr}: {getattr(self, attr)}") + + +class Version: + """ + Parse the versions of the modules used in the script. + """ + + @staticmethod + def get_versions(modules: list) -> dict: + """ + This function takes a list of modules and returns a dictionary with the + versions of each module. + """ + return {module.__name__: module.__version__ for module in modules} + + @staticmethod + def format_yaml_like(data: dict, indent: int = 0) -> str: + """ + Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + yaml_str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{Version.format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + + +class MyGene: + """ + This class will query the MyGene.info API and retrieve the go terms + associated with a list of gene ids. + + In concrete, if first queries the mygene API to get the mygene ids for each + of the query gene. Then, it queries for the annotations, and parses the go + terms all together with all the other information. + """ + def __init__(self, query: list, species: str, scopes: str, entrezonly: bool, ensemblonly: bool, go_category: str = None, go_evidence: str = None) -> None: + self.query = query + self.fields = "go,symbol,name,taxid" + self.species = species + self.scopes = scopes + self.entrezonly = entrezonly + self.ensemblonly = ensemblonly + self.go_category = go_category + self.go_evidence = go_evidence + self.mg = mygene.MyGeneInfo() + self.idmap = self.query2idmap() + print(f"fetched {len(self.idmap)} ids from {len(self.query)} queries") + + def query2idmap(self) -> dict: + """ + It returns a dictionary with the mygene ids as keys and the query ids as values. + """ + q = self.mg.querymany( + self.query, + scopes=self.scopes, + species=self.species, + entrezonly=self.entrezonly, + ensemblonly=self.ensemblonly, + returnall=True + ) + return {dic['_id']: dic['query'] for dic in q['out'] if '_id' in dic} + + def id2info(self) -> list: + """ + It returns a list of dictionaries with the info returned from getgenes for all the query ids. + Each dictionary contains the annotations for the corresponding query gene. + """ + return self.mg.getgenes(list(set(self.idmap)), fields=self.fields, species=self.species) + + def parse_go_based_info(self) -> dict: + """ + It queries the annotations for all query ids and then parses a go + centric dictionary. It is a dictionary of dictionaries with the + following format: {{go_id1: [go_term, gene1, gene2, ...]}, ...} + """ + info = {} + for dic in self.id2info(): + + if 'go' not in dic: + continue + if self.go_category: + dic['go'] = {category: dic['go'][category] for category in self.go_category.split(",") if category in dic['go']} + for category, go_list in dic['go'].items(): + if not isinstance(go_list, list): + go_list = [go_list] + for go in go_list: + if (self.go_evidence) and (go['evidence'] not in self.go_evidence.split(",")): + continue + + if go['id'] not in info: + info[go['id']] = [go['term'], self.idmap[dic['_id']]] + else: + info[go['id']].append(self.idmap[dic['_id']]) + return info + + def parse_gene_based_info(self) -> dict: + """ + It queries the annotations for all query ids and then parses a go + centric dictionary. + + At the end it returns a dictionary {query gene: {}} of dictionaries + with the following keys: query, mygene_id, go_id, go_term, go_evidence, + go_category, symbol, name, taxid. + """ + info = {} + for dic in self.id2info(): + + if 'go' not in dic: + continue + if self.go_category: + dic['go'] = {category: dic['go'][category] for category in self.go_category.split(",") if category in dic['go']} + for category, go_list in dic['go'].items(): + if not isinstance(go_list, list): + go_list = [go_list] + for go in go_list: + if (self.go_evidence) and (go['evidence'] not in self.go_evidence.split(",")): + continue + + current_info = { + 'query': self.idmap[dic['_id']], + 'mygene_id': dic['_id'], + 'go_id': go['id'], + 'go_term': go['term'], + 'go_evidence': go['evidence'], + 'go_category': category, + 'symbol': dic['symbol'], + 'name': dic['name'], + 'taxid': dic['taxid'] + } + info[self.idmap[dic['_id']]] = current_info + return info + + def parse_and_save_to_gmt(self, filename: str) -> list: + """ + It parses and saves go centric information to a gmt file. + The final gmt output will be sorted following the go id order. + """ + info = self.parse_go_based_info() + info = dict(sorted(info.items(), key=lambda x: x[0])) + with open(filename, 'w') as f: + for go_id, go_list in info.items(): + tmp = sorted(go_list[1:]) + f.write(go_id + "\\t" + go_list[0] + "\\t" + "\\t".join(tmp) + "\\n") + print(f"saved {len(info)} go terms to {filename}") + + def parse_and_save_to_tsv(self, filename: str) -> None: + """ + It parses and saves gene centric information in a tsv file. + The final tsv output will be sorted following the input query gene list order. + """ + info = self.parse_gene_based_info() + with open(filename, 'w') as f: + f.write("\\t".join(info[self.query[0]].keys()) + "\\n") + for gene in self.query: # sorted by query gene list + if gene in info: + f.write("\\t".join([str(val) for val in info[gene].values()]) + "\\n") + print(f"saved {len(info)} gene centric info to {filename}") + + +def load_list(filename: str, columname: str) -> list: + """ + It loads the list of gene ids from a file. + The columname is the name of the column where the gene ids are stored. + """ + if filename.split('.')[-1] == 'tsv': + sep = "\\t" + elif filename.split('.')[-1] == 'csv': + sep = "," + else: + raise ValueError("The input file extension should be either tsv or csv.") + with open(filename, 'r') as f: + idx = f.readline().strip().split(sep).index(columname) + return [line.strip().split(sep)[idx] for line in f] + + +if __name__ == "__main__": + + # parse and print arguments + args = Arguments() + args.print_args() + + # load gene list + gene_list = load_list(args.input, args.columname) + + # run mygene api + mg = MyGene( + gene_list, + species=args.species, + scopes=args.scopes, + entrezonly=args.entrezonly, + ensemblonly=args.ensemblonly, + go_category=args.go_category, + go_evidence=args.go_evidence + ) + + # parse annotations and save output files + mg.parse_and_save_to_gmt(args.output_gmt) + if args.generate_tsv: + mg.parse_and_save_to_tsv(args.output_tsv) + + # write versions to file + versions_this_module = {} + versions_this_module["${task.process}"] = Version.get_versions([argparse, mygene]) + with open("versions.yml", "w") as f: + f.write(Version.format_yaml_like(versions_this_module)) diff --git a/modules/nf-core/mygene/tests/default_tsv.config b/modules/nf-core/mygene/tests/default_tsv.config new file mode 100644 index 00000000..08bd6fac --- /dev/null +++ b/modules/nf-core/mygene/tests/default_tsv.config @@ -0,0 +1,3 @@ +process{ + ext.args = "--generate_tsv true" +} \ No newline at end of file diff --git a/modules/nf-core/mygene/tests/go_category.config b/modules/nf-core/mygene/tests/go_category.config new file mode 100644 index 00000000..771f8f4d --- /dev/null +++ b/modules/nf-core/mygene/tests/go_category.config @@ -0,0 +1,3 @@ +process { + ext.args = "--go_category bp,mf" +} \ No newline at end of file diff --git a/modules/nf-core/mygene/tests/go_evidence.config b/modules/nf-core/mygene/tests/go_evidence.config new file mode 100644 index 00000000..b19de214 --- /dev/null +++ b/modules/nf-core/mygene/tests/go_evidence.config @@ -0,0 +1,3 @@ +process { + ext.args = "--go_evidence EXP,IDA" +} \ No newline at end of file diff --git a/modules/nf-core/mygene/tests/main.nf.test b/modules/nf-core/mygene/tests/main.nf.test new file mode 100644 index 00000000..e5ba64ca --- /dev/null +++ b/modules/nf-core/mygene/tests/main.nf.test @@ -0,0 +1,106 @@ +nextflow_process { + + name "Test Process MYGENE" + script "../main.nf" + process "MYGENE" + + tag "modules" + tag "modules_nfcore" + tag "mygene" + + test("mygene - default options") { + + tag "default" + + when { + process { + """ + input[0] = [ + [id : 'test'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv") + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.gmt).match("mygene - default options - gmt") }, + { assert snapshot(process.out.versions).match("mygene - default options - versions") } + ) + } + } + + test("mygene - default with tsv file") { + + tag "default_with_tsv" + config "./default_tsv.config" + + when { + process { + """ + input[0] = [ + [id : 'test'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv") + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.gmt).match("mygene - default with tsv file - gmt") }, + { assert snapshot(process.out.tsv).match("mygene - default with tsv file - tsv") }, + { assert snapshot(process.out.versions).match("mygene - default with tsv file - versions") } + ) + } + } + + test("mygene - filter by go category") { + + tag "filter_by_go_category" + config "./go_category.config" + + when { + process { + """ + input[0] = [ + [id : 'test'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv") + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.gmt).match("mygene - filter by go category - gmt") }, + { assert snapshot(process.out.versions).match("mygene - filter by go category - versions") } + ) + } + } + + test("mygene - filter by go evidence") { + + tag "filter_by_go_evidence" + config "./go_evidence.config" + + when { + process { + """ + input[0] = [ + [id : 'test'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv") + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.gmt).match("mygene - filter by go evidence - gmt") }, + { assert snapshot(process.out.versions).match("mygene - filter by go evidence - versions") } + ) + } + } +} diff --git a/modules/nf-core/mygene/tests/main.nf.test.snap b/modules/nf-core/mygene/tests/main.nf.test.snap new file mode 100644 index 00000000..d6a334c7 --- /dev/null +++ b/modules/nf-core/mygene/tests/main.nf.test.snap @@ -0,0 +1,135 @@ +{ + "mygene - filter by go evidence - versions": { + "content": [ + [ + "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T17:20:31.854823" + }, + "mygene - default options - versions": { + "content": [ + [ + "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T17:19:43.081388" + }, + "mygene - default with tsv file - versions": { + "content": [ + [ + "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T17:20:01.837699" + }, + "mygene - default options - gmt": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.gmt:md5,d76d4d06dad199c5e3ecef7060876834" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T17:19:43.060437" + }, + "mygene - filter by go category - versions": { + "content": [ + [ + "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T17:20:17.233994" + }, + "mygene - filter by go evidence - gmt": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.gmt:md5,da6b31a5f889e3aedb16b4154f9652af" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T17:20:31.827798" + }, + "mygene - default with tsv file - tsv": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tsv:md5,018e23173b224cbf328751006593900e" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T17:20:01.81872" + }, + "mygene - default with tsv file - gmt": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.gmt:md5,d76d4d06dad199c5e3ecef7060876834" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T17:20:01.79811" + }, + "mygene - filter by go category - gmt": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.gmt:md5,213c1d1d2345df8ea51d67cb1670f4f7" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T17:20:17.208509" + } +} \ No newline at end of file diff --git a/modules/nf-core/mygene/tests/tags.yml b/modules/nf-core/mygene/tests/tags.yml new file mode 100644 index 00000000..c867c978 --- /dev/null +++ b/modules/nf-core/mygene/tests/tags.yml @@ -0,0 +1,2 @@ +mygene: + - "modules/nf-core/mygene/**" diff --git a/modules/nf-core/propr/grea/environment.yml b/modules/nf-core/propr/grea/environment.yml new file mode 100644 index 00000000..c6897c73 --- /dev/null +++ b/modules/nf-core/propr/grea/environment.yml @@ -0,0 +1,7 @@ +name: propr_grea +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::r-propr=5.0.4 diff --git a/modules/nf-core/propr/grea/main.nf b/modules/nf-core/propr/grea/main.nf new file mode 100644 index 00000000..66cf3c05 --- /dev/null +++ b/modules/nf-core/propr/grea/main.nf @@ -0,0 +1,24 @@ +process PROPR_GREA { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/r-propr:5.0.4': + 'quay.io/biocontainers/r-propr:5.0.4' }" + + input: + tuple val(meta), path(adj) + tuple val(meta2), path(gmt) + + output: + tuple val(meta), path("*.go.tsv"), emit: enrichedGO + path "versions.yml", emit: versions + path "*.R_sessionInfo.log", emit: session_info + + when: + task.ext.when == null || task.ext.when + + script: + template 'grea.R' +} diff --git a/modules/nf-core/propr/grea/meta.yml b/modules/nf-core/propr/grea/meta.yml new file mode 100644 index 00000000..de40abd3 --- /dev/null +++ b/modules/nf-core/propr/grea/meta.yml @@ -0,0 +1,57 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "propr_grea" +description: Perform Gene Ratio Enrichment Analysis +keywords: + - logratio + - differential + - propr + - grea + - enrichment + - expression +tools: + - "grea": + description: "Gene Ratio Enrichment Analysis" + homepage: "https://github.com/tpq/propr" + documentation: "https://rdrr.io/cran/propr/man/propr.html" + tool_dev_url: "https://github.com/tpq/propr" + doi: "10.2202/1544-6115.1175" + licence: ["GPL-2"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the knowledge database + - adj: + type: file + description: adjacency matrix for gene ratio proportionality/differential proportionality + pattern: "*.{csv,tsv}" + - gmt: + type: file + description: relational database containing genes and GO terms (generated by mygene module) + pattern: "*.{gmt}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - enrichedGO: + type: file + description: File containing GO terms and their enrichment values + pattern: "*.{csv}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@caraiz2001" +maintainers: + - "@caraiz2001" diff --git a/modules/nf-core/propr/grea/templates/grea.R b/modules/nf-core/propr/grea/templates/grea.R new file mode 100644 index 00000000..6e1c6a00 --- /dev/null +++ b/modules/nf-core/propr/grea/templates/grea.R @@ -0,0 +1,253 @@ +#!/usr/bin/env Rscript + +################################################ +################################################ +## Functions ## +################################################ +################################################ + +#' Parse out options from a string without recourse to optparse +#' +#' @param x Long-form argument list like --opt1 val1 --opt2 val2 +#' +#' @return named list of options and values similar to optparse +parse_args <- function(x){ + args_list <- unlist(strsplit(x, ' ?--')[[1]])[-1] + args_vals <- lapply(args_list, function(x) scan(text=x, what='character', quiet = TRUE)) + + # Ensure the option vectors are length 2 (key/ value) to catch empty ones + args_vals <- lapply(args_vals, function(z){ length(z) <- 2; z}) + + parsed_args <- structure(lapply(args_vals, function(x) x[2]), names = lapply(args_vals, function(x) x[1])) + parsed_args[! is.na(parsed_args)] +} + +#' Flexibly read CSV or TSV files (determined by file extension) +#' +#' @param file Input file +#' @param header Boolean. TRUE if first row is header. False without header. +#' @param row.names The first column is used as row names by default. +#' Otherwise, give another number. Or use NULL when no row.names are present. +#' +#' @return output Data frame +read_delim_flexible <- function(file, header = TRUE, row.names = 1, check.names = TRUE){ + + ext <- tolower(tail(strsplit(basename(file), split = "\\\\.")[[1]], 1)) # Get the file extension + + if (ext == "tsv" || ext == "txt") { # If the file is a tsv or txt file + separator <- "\\t" # Set the separator variable to tab + } else if (ext == "csv") { # If the file is a csv file + separator <- "," + } else { + stop(paste("Unknown separator for", ext)) + } + + mat <- read.delim( # Read the file + file, + sep = separator, # Set the separator defined above + header = header, + row.names = row.names, + check.names = check.names + ) +} + +#' Converts the .gmt file into a df +#' +#' @param file_gmt_path path of the .gmt file provided by mygene module. +#' @return output dataframe a Dataframe: 1st column = GOterm, 2nd = Description, 3d to end = genes. +process_gmt_file <- function(file_gmt_path) { + + lines <- readLines(file_gmt_path) + data_list <- list() + + for (line in lines) { + fields <- strsplit(line, "\\t")[[1]] # Split the line based on the tab character + go_term <- fields[1] # Extract the GO term + + # Create a data frame with the GO term in the first column + # Fill in missing values with NA to ensure consistent column lengths + data_list[[go_term]] <- data.frame(GOterm = go_term, + Description = fields[2], + GeneIDs = c(fields[3:length(fields)], rep(NA, max(0, 3 - length(fields))))) + } + + gmt_df <- do.call(rbind, data_list) # Combine all data frames into a single data frame + gmt_df\$GeneIDs <- as.character(gmt_df\$GeneIDs) # Convert gene IDs to character to avoid coercion + + return(gmt_df) +} + +#' Converts the .gmt data frame into a knowledge matrix (contingency table) +#' +#' @param gmt_df .gmt df created by process_gmt_file +#' @return output dataframe. A knowledge database where each row is a graph node (gene) +#' and each column is a concept (GO term). +gmt_to_K<- function(gmt_df){ + + summ_df <- as.data.frame(gmt_df\$GeneIDs) + summ_df <- cbind(summ_df, as.data.frame(gmt_df\$GOterm)) + colnames(summ_df)<- c("GeneIDs", "GOterm") + summ_df<- unique(summ_df) + + summ_df\$value <- 1 + + K <- table(summ_df\$GeneIDs, summ_df\$GOterm) + K <- as.data.frame.matrix(K) + + return(K) +} + +#' Expands knowledge matrix with missing genes to ensure same number of rows for A and K +#' +#' @param adjacency_matrix gene x gene correlation or proportionality adjacency matrix (output propr/propd) +#' @return output dataframe. A knowledge database where each row is a graph node (gene) +#' and each column is a concept (GO term). +add_missing <- function(adjacency_matrix, knowledge_matrix){ + + missing_genes <- setdiff(rownames(adjacency_matrix), rownames(knowledge_matrix)) + extra_rows <- data.frame(matrix(0, nrow = length(missing_genes), ncol = ncol(knowledge_matrix))) + rownames(extra_rows) <- missing_genes + colnames(extra_rows) <- colnames(knowledge_matrix) + + knowledge_matrix <- rbind(knowledge_matrix, extra_rows) + return(knowledge_matrix) +} + +################################################ +################################################ +## Parse arguments ## +################################################ +################################################ + +opt <- list( + adj = '$adj', + gmt = '$gmt', + prefix = ifelse('$task.ext.prefix' == 'null', '$meta.pathway_name', '$task.ext.prefix'), + permutation = 10, + fixseed = TRUE, + ncores = as.integer('$task.cpus') +) + +opt_types <- list( + adj = 'character', + gmt = 'character', + prefix = 'character', + permutation = 'numeric', + fixseed = 'logical', + ncores = 'numeric' +) + +# Apply parameter overrides +args_opt <- parse_args('$task.ext.args') + +for ( ao in names(args_opt)){ + if (! ao %in% names(opt)){ + stop(paste("Invalid option:", ao)) + } else { + + # Preserve classes from defaults where possible + if (! is.null(opt[[ao]])){ + args_opt[[ao]] <- as(args_opt[[ao]], opt_types[[ao]]) + } + # set NA + if (args_opt[[ao]] %in% c('NA', NA, 'null')){ + args_opt[[ao]] <- NA + } + opt[[ao]] <- args_opt[[ao]] + } +} + +# Check if required parameters have been provided +required_opts <- c('adj', 'gmt') # defines a vector required_opts containing the names of the required parameters. +missing <- required_opts[unlist(lapply(opt[required_opts], is.null)) | ! required_opts %in% names(opt)] +if (length(missing) > 0){ + stop(paste("Missing required options:", paste(missing, collapse=', '))) +} + + +# Check file inputs are valid +for (file_input in c('adj', 'gmt')){ + if (is.null(opt[[file_input]])) { + stop(paste("Please provide", file_input), call. = FALSE) + } + if (! file.exists(opt[[file_input]])){ + stop(paste0('Value of ', file_input, ': ', opt[[file_input]], ' is not a valid file')) + } +} + +################################################ +################################################ +## Finish loading libraries ## +################################################ +################################################ + +library(propr) + +################################################ +################################################ +## Enrichment analysis ## +################################################ +################################################ + +# Read gene x gene adjacency matrix +A <- read_delim_flexible(opt\$adj, header = TRUE, row.names = 1, check.names = TRUE) + +# Read and process gene x GO term matrix +gmt_df <- process_gmt_file(opt\$gmt) +K <- gmt_to_K(gmt_df) + +# Ensure same number of rows (genes) +if (nrow(A) != nrow(K)){ + K <- add_missing(A, K) +} + +# Run Graflex +G <- runGraflex(A, K, opt\$permutation, opt\$fixseed) + +################################################ +################################################ +## Generate outputs ## +################################################ +################################################ + +write.table( + G, + file = paste0(opt\$prefix, '.go.tsv'), + col.names = TRUE, + row.names = TRUE, # False + sep = '\\t', + quote = FALSE + +) + +################################################ +################################################ +## R SESSION INFO ## +################################################ +################################################ + +sink(paste0(opt\$prefix, ".R_sessionInfo.log")) +print(sessionInfo()) +sink() + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +r.version <- strsplit(version[['version.string']], ' ')[[1]][3] +propr.version <- as.character(packageVersion('propr')) + +writeLines( + c( + '"${task.process}":', + paste(' r-base:', r.version), + paste(' r-propr:', propr.version) + ), +'versions.yml') + +################################################ +################################################ +################################################ +################################################ diff --git a/modules/nf-core/propr/grea/tests/grea_test.config b/modules/nf-core/propr/grea/tests/grea_test.config new file mode 100644 index 00000000..8d0d229a --- /dev/null +++ b/modules/nf-core/propr/grea/tests/grea_test.config @@ -0,0 +1,8 @@ +process { + withName: "PROPR_PROPR"{ + ext.args = { "--adjacency true --permutation 5 --fixseed true --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05"} + } + withName: "PROPR_GREA"{ + ext.args = { "--permutation 5 --fixseed true"} + } +} \ No newline at end of file diff --git a/modules/nf-core/propr/grea/tests/main.nf.test b/modules/nf-core/propr/grea/tests/main.nf.test new file mode 100644 index 00000000..afac1dec --- /dev/null +++ b/modules/nf-core/propr/grea/tests/main.nf.test @@ -0,0 +1,62 @@ +nextflow_process { + + name "Test Process PROPR_GREA" + script "../main.nf" + process "PROPR_GREA" + + tag "modules" + tag "modules_nfcore" + tag "propr" + tag "propr/grea" + tag "mygene" + tag "propr/propr" + + test("grea chained to propr using default options") { + + tag "default" + config "./grea_test.config" + + setup { + run("PROPR_PROPR") { + script "../../propr/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") + ] + """ + } + } + run("MYGENE") { + script "../../../mygene/main.nf" + process { + """ + input[0] = [ + [id : 'test'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv") + ] + """ + } + } + } + + when { + process { + """ + input[0] = PROPR_PROPR.out.adj.collect{ meta, adj -> adj }.map{ adj -> [[ id: 'test_adj'], adj]} + input[1] = MYGENE.out.gmt.collect{ meta, gmt -> gmt }.map{ gmt -> [[ id: 'test_gmt'], gmt]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.enrichedGO).match("grea chained to propr using default options - enrichedGO") }, + { assert snapshot(process.out.versions).match("versions") } + + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/propr/grea/tests/main.nf.test.snap b/modules/nf-core/propr/grea/tests/main.nf.test.snap new file mode 100644 index 00000000..a915603d --- /dev/null +++ b/modules/nf-core/propr/grea/tests/main.nf.test.snap @@ -0,0 +1,31 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,222a7a8b79b5a2987637279847c609d1" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T10:45:07.582509" + }, + "grea chained to propr using default options - enrichedGO": { + "content": [ + [ + [ + { + "id": "test_adj" + }, + "test_adj.go.tsv:md5,914d8b750ba303a297efb7331ec238b7" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T10:45:07.508934" + } +} \ No newline at end of file diff --git a/modules/nf-core/propr/grea/tests/tags.yml b/modules/nf-core/propr/grea/tests/tags.yml new file mode 100644 index 00000000..e7f80baf --- /dev/null +++ b/modules/nf-core/propr/grea/tests/tags.yml @@ -0,0 +1,2 @@ +propr/grea: + - "modules/nf-core/propr/grea/**" diff --git a/modules/nf-core/propr/propd/environment.yml b/modules/nf-core/propr/propd/environment.yml new file mode 100644 index 00000000..058f30a0 --- /dev/null +++ b/modules/nf-core/propr/propd/environment.yml @@ -0,0 +1,7 @@ +name: propr_propd +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::r-propr=5.0.3 diff --git a/modules/nf-core/propr/propd/main.nf b/modules/nf-core/propr/propd/main.nf new file mode 100644 index 00000000..d7ada4ab --- /dev/null +++ b/modules/nf-core/propr/propd/main.nf @@ -0,0 +1,28 @@ +process PROPR_PROPD { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/r-propr:5.0.3': + 'quay.io/biocontainers/r-propr:5.0.3' }" + + input: + tuple val(meta), path(count) + tuple val(meta2), path(samplesheet) + + output: + tuple val(meta), path("*.propd.rds"), emit: propd + tuple val(meta), path("*.propd.tsv"), emit: results + tuple val(meta), path("*.fdr.tsv") , emit: fdr , optional:true + tuple val(meta), path("*.adj.csv"), emit: adj , optional:true + path "*.warnings.log", emit: warnings + path "*.R_sessionInfo.log" , emit: session_info + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'propd.R' +} diff --git a/modules/nf-core/propr/propd/meta.yml b/modules/nf-core/propr/propd/meta.yml new file mode 100644 index 00000000..1c408d73 --- /dev/null +++ b/modules/nf-core/propr/propd/meta.yml @@ -0,0 +1,68 @@ +name: "propr_propd" +description: Perform differential proportionality analysis +keywords: + - differential + - proportionality + - logratio + - expression + - propr +tools: + - "propr": + description: "Logratio methods for omics data" + homepage: "https://github.com/tpq/propr" + documentation: "https://rdrr.io/cran/propr/man/propr.html" + tool_dev_url: "https://github.com/tpq/propr" + doi: "10.1038/s41598-017-16520-0" + licence: ["GPL-2"] +input: + - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - count: + type: file + description: | + Count matrix, where rows = variables or genes, columns = samples or cells. + This matrix should not contain zeros. One should plug this module after another one that handles the zeros. + pattern: "*.{csv,tsv}" + - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the sample sheet and matrix + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata +output: + - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - propd: + type: file + description: R propd object + pattern: "*.propd.rds" + - results: + type: file + description: Results table + pattern: "*.propd.tsv" + - fdr: + type: file + description: (optional) propr fdr table + pattern: "*.fdr.tsv" + - session_info: + type: file + description: dump of R SessionInfo + pattern: "*.R_sessionInfo.log" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@suzannejin" +maintainers: + - "@suzannejin" diff --git a/modules/nf-core/propr/propd/templates/propd.R b/modules/nf-core/propr/propd/templates/propd.R new file mode 100644 index 00000000..1bdae252 --- /dev/null +++ b/modules/nf-core/propr/propd/templates/propd.R @@ -0,0 +1,372 @@ +#!/usr/bin/env Rscript + + +################################################ +################################################ +## Functions ## +################################################ +################################################ + +#' Parse out options from a string without recourse to optparse +#' +#' @param x Long-form argument list like --opt1 val1 --opt2 val2 +#' +#' @return named list of options and values similar to optparse + +parse_args <- function(x){ + args_list <- unlist(strsplit(x, ' ?--')[[1]])[-1] + args_vals <- lapply(args_list, function(x) scan(text=x, what='character', quiet = TRUE)) + + # Ensure the option vectors are length 2 (key/ value) to catch empty ones + args_vals <- lapply(args_vals, function(z){ length(z) <- 2; z}) + + parsed_args <- structure(lapply(args_vals, function(x) x[2]), names = lapply(args_vals, function(x) x[1])) + parsed_args[! is.na(parsed_args)] +} + +#' Flexibly read CSV or TSV files +#' +#' @param file Input file +#' @param header Boolean. TRUE if first row is header. False without header. +#' @param row.names The first column is used as row names by default. +#' Otherwise, give another number. Or use NULL when no row.names are present. +#' +#' @return output Data frame +read_delim_flexible <- function(file, header = TRUE, row.names = 1, check.names = TRUE){ + + ext <- tolower(tail(strsplit(basename(file), split = "\\\\.")[[1]], 1)) + + if (ext == "tsv" || ext == "txt") { + separator <- "\\t" + } else if (ext == "csv") { + separator <- "," + } else { + stop(paste("Unknown separator for", ext)) + } + + mat <- read.delim( + file, + sep = separator, + header = header, + row.names = row.names, + check.names = check.names + ) + + if (!is.null(row.names)){ + if ( (row.names == 'gene_id') & ('gene_name' %in% colnames(mat)) ){ + mat <- mat[, -which(colnames(mat) == 'gene_name')] + } else if ( (row.names == 'gene_name') & ('gene_id' %in% colnames(mat)) ){ + mat <- mat[, -which(colnames(mat) == 'gene_id')] + } + } + + return(mat) +} + +#' Extract the values for a single metric and convert it into a genes x genes matrix. +#' +#' @param object propd object +one_metric_df <- function(object) { + results <- getResults(object) + #keep only the metric of interest + one_metric <- cbind(results\$Partner, results\$Pair, results\$theta) + colnames(one_metric) <- c("Partner", "Pair", "theta") + one_metric <- as.data.frame(one_metric) + + # Extract the unique gene names + gene_names <- sort(unique(c(one_metric\$Partner, one_metric\$Pair))) + # Initialize a square matrix with NA + square_matrix <- matrix(NA, nrow = length(gene_names), ncol = length(gene_names)) + rownames(square_matrix) <- gene_names + colnames(square_matrix) <- gene_names + + # Use the `match` function to get the row and column indices + row_indices <- match(one_metric\$Partner, gene_names) + col_indices <- match(one_metric\$Pair, gene_names) + # Use these indices to populate the matrix + square_matrix[cbind(row_indices, col_indices)] <- one_metric[["theta"]] + # Populate the reverse pairs to ensure symmetry + square_matrix[cbind(col_indices, row_indices)] <- one_metric[["theta"]] + return(square_matrix) +} + +#' Extract the differential proportionality cutoff for a specified FDR value. +#' Gene pairs with a value higher than the extracted cutoff will be considered significantly differentially proportional. +#' +#' @param object propd object. Output from propd function. updateCutoffs function should be applied to the object previous to valCutoff. +#' @param fdrVal FDR value to extract the cutoff for. Per default 0.05. +#' +#' @return cutoff value. Differential proportionality values lower than this cutoff are considered significant. +valCutoff <- function(object, fdrVal = 0.05){ + fdr_df <- object@fdr + if (prod(dim(fdr_df) == 0)){ + warning("Please run updateCutoff on propd first") + }else{ + fdr_vals <- fdr_df\$FDR + if (any(!is.na(fdr_vals))){ # Si hay algun valor de FDR correcto + threshold <- any(fdr_vals <= fdrVal) + if (threshold){ + fdr_threshold <- fdr_vals[which.min(fdr_vals <= fdrVal) - 1] + }else{ + warning("FDR is higher than the specified threshold for all proportionality values. Using the lowest fdr instead") + fdr_threshold <- fdr_vals[1] + } + }else{ + stop("No true counts in the given interval. FDR values are not defined") + geterrmessage() + } + } + cutoff <- fdr_df\$cutoff[fdr_df\$FDR == fdr_threshold] + return(cutoff) +} + +#' Convert a proportionality matrix to an adjacency matrix based on a threshold. +#' +#' @param matrix proportionality matrix. Can be extracted from propr object with getMatrix(). +#' @param cutoff Significant proportionality value extracted from valCutoff function. +#' +#' @return Adjacency matrix. Gene pairs with a proportionality value lower than the threshold will have 1, otherwise 0. +convert_to_adjacency <- function(matrix, cutoff) { + adjacency <- ifelse(matrix < cutoff, 1, 0) + return(adjacency) +} + +################################################ +################################################ +## Parse arguments ## +################################################ +################################################ + +opt <- list( + prefix = ifelse('$task.ext.prefix' == 'null','$meta.pathway_name', '$task.ext.prefix'), + count = '$count', + samplesheet = '$samplesheet', + features_id_col = 'gene_id', # column name of feature ids + obs_id_col = 'sample', # column name of observation ids + group_col = 'treatment', # column name of grouping variable + metric = 'theta_d', # differential proportionality metric: theta_d, theta_e or theta_f + alpha = NA, # alpha for boxcox transformation + permutation = 0, # permutation cycles for computing FDR + cutoff_min = 0.05, # minimun threshold to test + cutoff_max = 0.95, # maximun threshold to test + cutoff_interval = 0.05, # interval between thresholds + fixseed = FALSE, + adjacency = FALSE, + fdrVal = 0.05, + ncores = as.integer('$task.cpus') +) +opt_types <- list( + prefix = 'character', + count = 'character', + samplesheet = 'character', + features_id_col = 'character', + obs_id_col = 'character', + group_col = 'character', + metric = 'character', + alpha = 'numeric', + permutation = 'numeric', + cutoff_min = 'numeric', + cutoff_max = 'numeric', + cutoff_interval = 'numeric', + fixseed = 'logical', + adjacency = 'logical', + fdrVal = 'numeric', + ncores = 'numeric' +) + +# Apply parameter overrides +args_opt <- parse_args('$task.ext.args') +for ( ao in names(args_opt)){ + if (! ao %in% names(opt)){ + stop(paste("Invalid option:", ao)) + } else { + + # Preserve classes from defaults where possible + if (! is.null(opt[[ao]])){ + args_opt[[ao]] <- as(args_opt[[ao]], opt_types[[ao]]) + } + # set NA + if (args_opt[[ao]] %in% c('NA', NA, 'null')){ + args_opt[[ao]] <- NA + } + opt[[ao]] <- args_opt[[ao]] + } +} + +# Check if required parameters have been provided +required_opts <- c('count','samplesheet') +missing <- required_opts[unlist(lapply(opt[required_opts], is.null)) | ! required_opts %in% names(opt)] +if (length(missing) > 0){ + stop(paste("Missing required options:", paste(missing, collapse=', '))) +} + +# Check file inputs are valid +for (file_input in c('count','samplesheet')){ + if (is.null(opt[[file_input]])) { + stop(paste("Please provide", file_input), call. = FALSE) + } + if (! file.exists(opt[[file_input]])){ + stop(paste0('Value of ', file_input, ': ', opt[[file_input]], ' is not a valid file')) + } +} + +# check parameters +if (! opt\$metric %in% c('theta_d', 'theta_e', 'theta_f')) stop('Please provide a valid differential proportionality metric') + +################################################ +################################################ +## Finish loading libraries ## +################################################ +################################################ + +library(propr) + +################################################ +################################################ +## Perform differential proportionality ## +################################################ +################################################ + +# read matrix +mat <- read_delim_flexible( + opt\$count, + header = TRUE, + row.names = opt\$features_id_col, + check.names = FALSE +) +mat <- t(mat) + +# check zeros +# log transformation should be applied on non-zero data +# otherwise Inf values are generated +if (any(mat == 0)) print("Zeros will be replaced by minimun value before logratio analysis") + +# parse group +# this creates a vector referring to the group id for each observation +samplesheet <- read_delim_flexible( + opt\$samplesheet, + header = TRUE, + row.names = NULL, + check.names = FALSE +) +tmp <- samplesheet[[opt\$group_col]] +names(tmp) <- samplesheet[[opt\$obs_id_col]] +group <- as.vector(tmp[rownames(mat)]) +if (length(group) != nrow(mat)) stop('Error when parsing group') + +# perform differential proportionality +pd <- propd( + mat, + group = group, + alpha = opt\$alpha, + weighted = FALSE, + p = opt\$permutation, + fixseed = opt\$fixseed +) + +if (opt\$metric == 'theta_d'){ + pd <- setDisjointed(pd) +} else if (opt\$metric == 'theta_e'){ + pd <- setEmergent(pd) +} else if (opt\$metric == 'theta_f'){ + pd <- setActive(pd, what = "theta_f") +} + +# update FDR by permutation, if required +if (opt\$permutation > 0) { + cutoff <- seq( + opt\$cutoff_min, + opt\$cutoff_max, + opt\$cutoff_interval + ) + pd <- updateCutoffs(pd, cutoff=cutoff, ncores=opt\$ncores) + if (opt\$metric == 'theta_d') pd <- updateF(pd) +} + +# Extract adjacency matrix if required +if (opt\$adjacency == TRUE) { + matrix <- one_metric_df(pd) + cutoff <- valCutoff(pd, opt\$fdrVal) + adj <- convert_to_adjacency(matrix, cutoff) +} + +################################################ +################################################ +## Generate outputs ## +################################################ +################################################ + +saveRDS( + pd, + file = paste0(opt\$prefix, '.propd.rds') +) + +write.table( + getResults(pd), + file = paste0(opt\$prefix, '.propd.tsv'), + col.names = TRUE, + row.names = FALSE, + sep = '\\t', + quote = FALSE +) + +if (opt\$permutation > 0) { + write.table( + pd@fdr, + file = paste0(opt\$prefix, '.fdr.tsv'), + col.names = TRUE, + sep = '\\t', + quote = FALSE + ) +} + +if (opt\$adjacency == TRUE) { + write.table( + adj, + file = paste0(opt\$prefix, '.adj.csv'), + col.names = TRUE, + row.names = TRUE, + sep = ',', + quote = FALSE + ) +} + +################################################ +################################################ +## WARNINGS ## +################################################ +################################################ + +sink(paste0(opt\$prefix, ".warnings.log")) +print(warnings()) +sink() + +################################################ +################################################ +## R SESSION INFO ## +################################################ +################################################ + +sink(paste0(opt\$prefix, ".R_sessionInfo.log")) +print(sessionInfo()) +sink() + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +propr.version <- as.character(packageVersion('propr')) + +writeLines( + c( + '"${task.process}":', + paste(' r-propr:', propr.version) + ), +'versions.yml') + +################################################ +################################################ +################################################ +################################################ diff --git a/modules/nf-core/propr/propd/tests/adjacency.config b/modules/nf-core/propr/propd/tests/adjacency.config new file mode 100644 index 00000000..072a4d75 --- /dev/null +++ b/modules/nf-core/propr/propd/tests/adjacency.config @@ -0,0 +1,3 @@ +process { + ext.args = {"--permutation 10 --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.1 --fixseed true --adjacency true"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propd/tests/boxcox_theta_e.config b/modules/nf-core/propr/propd/tests/boxcox_theta_e.config new file mode 100755 index 00000000..40c0548d --- /dev/null +++ b/modules/nf-core/propr/propd/tests/boxcox_theta_e.config @@ -0,0 +1,4 @@ +process { + ext.args = {"--metric theta_e --alpha 0.2 --permutation 10 --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --fixseed true"} + ext.prefix = {"test+theta_e+0.2"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propd/tests/default_boxcox.config b/modules/nf-core/propr/propd/tests/default_boxcox.config new file mode 100755 index 00000000..831002d9 --- /dev/null +++ b/modules/nf-core/propr/propd/tests/default_boxcox.config @@ -0,0 +1,4 @@ +process { + ext.args = {"--alpha 0.2 --permutation 10 --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --fixseed true"} + ext.prefix = {"test+theta_d+0.2"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propd/tests/default_permutation.config b/modules/nf-core/propr/propd/tests/default_permutation.config new file mode 100755 index 00000000..e89c239f --- /dev/null +++ b/modules/nf-core/propr/propd/tests/default_permutation.config @@ -0,0 +1,4 @@ +process { + ext.args = {"--permutation 10 --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --fixseed true"} + ext.prefix = {"test+theta_d+NA"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propd/tests/main.nf.test b/modules/nf-core/propr/propd/tests/main.nf.test new file mode 100755 index 00000000..9fcaf93a --- /dev/null +++ b/modules/nf-core/propr/propd/tests/main.nf.test @@ -0,0 +1,154 @@ +nextflow_process { + + name "Test Process PROPR_PROPD" + script "../main.nf" + process "PROPR_PROPD" + + tag "modules" + tag "modules_nfcore" + tag "propr" + tag "propr/propd" + + test("Test propr/propd using default permutation") { + + tag "default" + config "./default_permutation.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") + ] + input[1] = [ + [ id: 'test'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv") + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.results).match("Test propr/propd using default permutation - results") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("Test propr/propd using default boxcox permutation") { + + tag "default_boxcox" + config "./default_boxcox.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") + ] + input[1] = [ + [ id: 'test'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv") + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.results).match(" Test propr/propd using default boxcox permutation - results") }, + { assert snapshot(process.out.fdr).match(" Test propr/propd using default boxcox permutation - fdr") } + ) + } + } + + test("Test propr/propd using theta_e permutation") { + + tag "theta_e" + config "./theta_e.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") + ] + input[1] = [ + [ id: 'test'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv") + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.results).match("Test propr/propd using theta_e permutation - results") } + ) + } + } + + test("Test propr/propd using theta_e and boxcox permutation") { + + tag "boxcox_theta_e" + config "./boxcox_theta_e.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") + ] + input[1] = [ + [ id: 'test'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv") + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.results).match("Test propr/propd using theta_e and boxcox permutation - results") } + ) + } + } + + test("Test propr/propd with adjacency matrix") { + + tag "adjacency" + config "./adjacency.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") + ] + input[1] = [ + [ id: 'test'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv") + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.adj).match("Test propr/propd with adjacency matrix - adj") }, + { assert snapshot(process.out.results).match(" - results") } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/propr/propd/tests/main.nf.test.snap b/modules/nf-core/propr/propd/tests/main.nf.test.snap new file mode 100644 index 00000000..58199b4b --- /dev/null +++ b/modules/nf-core/propr/propd/tests/main.nf.test.snap @@ -0,0 +1,133 @@ +{ + " Test propr/propd using default boxcox permutation - fdr": { + "content": [ + [ + [ + { + "id": "test" + }, + "test+theta_d+0.2.fdr.tsv:md5,17e1c382e5f8275e2858a86e98c1aa6c" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-16T11:55:35.703293" + }, + "Test propr/propd using theta_e and boxcox permutation - results": { + "content": [ + [ + [ + { + "id": "test" + }, + "test+theta_e+0.2.propd.tsv:md5,d56fcc7c8ae0b0853ea9ca6ac6484a08" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-16T11:59:33.28078" + }, + "Test propr/propd using theta_e permutation - results": { + "content": [ + [ + [ + { + "id": "test" + }, + "test+theta_e+NA.propd.tsv:md5,c190d80c11ba99a0303a8dd5ab8ed76f" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-16T11:57:24.038188" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,b41d17751970fc8bcf4f8e0326d239e2" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-16T11:53:45.165637" + }, + " - results": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.propd.tsv:md5,34fda117492faf9a60f5807f56c4be68" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-16T14:13:47.602525" + }, + " Test propr/propd using default boxcox permutation - results": { + "content": [ + [ + [ + { + "id": "test" + }, + "test+theta_d+0.2.propd.tsv:md5,f1886c538e6aeed1bbac4c8c1ef0c930" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-16T11:55:32.476341" + }, + "Test propr/propd using default permutation - results": { + "content": [ + [ + [ + { + "id": "test" + }, + "test+theta_d+NA.propd.tsv:md5,34fda117492faf9a60f5807f56c4be68" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-16T11:53:43.056295" + }, + "Test propr/propd with adjacency matrix - adj": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.adj.csv:md5,f9d19255f9400e6c4daa01f86d74f017" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-16T14:13:47.427246" + } +} \ No newline at end of file diff --git a/modules/nf-core/propr/propd/tests/tags.yml b/modules/nf-core/propr/propd/tests/tags.yml new file mode 100755 index 00000000..ba65ca0a --- /dev/null +++ b/modules/nf-core/propr/propd/tests/tags.yml @@ -0,0 +1,2 @@ +propr/propd: + - "modules/nf-core/propr/propd/**" diff --git a/modules/nf-core/propr/propd/tests/theta_e.config b/modules/nf-core/propr/propd/tests/theta_e.config new file mode 100755 index 00000000..37c0dd5a --- /dev/null +++ b/modules/nf-core/propr/propd/tests/theta_e.config @@ -0,0 +1,4 @@ +process { + ext.args = {"--metric theta_e --permutation 10 --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --fixseed true"} + ext.prefix = {"test+theta_e+NA"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propr/environment.yml b/modules/nf-core/propr/propr/environment.yml new file mode 100644 index 00000000..cb163068 --- /dev/null +++ b/modules/nf-core/propr/propr/environment.yml @@ -0,0 +1,7 @@ +name: propr_propr +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::r-propr=5.0.3 diff --git a/modules/nf-core/propr/propr/main.nf b/modules/nf-core/propr/propr/main.nf new file mode 100644 index 00000000..531e575c --- /dev/null +++ b/modules/nf-core/propr/propr/main.nf @@ -0,0 +1,27 @@ +process PROPR_PROPR { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/r-propr:5.0.3': + 'quay.io/biocontainers/r-propr:5.0.3' }" + + input: + tuple val(meta), path(count) + + output: + tuple val(meta), path("*.propr.rds"), emit: propr + tuple val(meta), path("*.propr.tsv"), emit: matrix + tuple val(meta), path("*.fdr.tsv"), emit: fdr , optional:true + tuple val(meta), path("*.adj.csv"), emit: adj , optional:true + path "*.warnings.log", emit: warnings + path "*.R_sessionInfo.log", emit: session_info + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'propr.R' +} diff --git a/modules/nf-core/propr/propr/meta.yml b/modules/nf-core/propr/propr/meta.yml new file mode 100644 index 00000000..c2c9a11d --- /dev/null +++ b/modules/nf-core/propr/propr/meta.yml @@ -0,0 +1,76 @@ +name: "propr_propr" +description: | + Perform logratio-based correlation analysis -> get proportionality & basis shrinkage partial correlation coefficients. + One can also compute standard correlation coefficients, if required. +keywords: + - coexpression + - correlation + - proportionality + - logratio + - propr + - corpcor + +tools: + - "propr": + description: "Logratio methods for omics data" + homepage: "https://github.com/tpq/propr" + documentation: "https://rdrr.io/cran/propr/man/propr.html" + tool_dev_url: "https://github.com/tpq/propr" + doi: "10.1038/s41598-017-16520-0" + licence: ["GPL-2"] + - "corpcor": + description: "Efficient Estimation of Covariance and (Partial) Correlation" + homepage: "https://cran.r-project.org/web/packages/corpcor/index.html" + documentation: "https://cran.r-project.org/web/packages/corpcor/corpcor.pdf" + doi: "10.2202/1544-6115.1175" + licence: ["GPL >=3"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - count: + type: file + description: | + Count matrix, where rows = variables or genes, columns = samples or cells. + This matrix should not contain zeros. Otherwise, they will be replaced by the minimun number. + It is recommended to handle the zeros beforehand with the method of preference. + pattern: "*.{csv,tsv}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - propr: + type: file + description: R propr object + pattern: "*.propr.rds" + - matrix: + type: file + description: Coefficient matrix + pattern: "*.propr.tsv" + - fdr: + type: file + description: (optional) propr fdr table + pattern: "*.fdr.tsv" + - adj: + type: file + description: (optional) propr adjacency table + pattern: "*.adj.csv" + - session_info: + type: file + description: dump of R SessionInfo + pattern: "*.R_sessionInfo.log" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@suzannejin" diff --git a/modules/nf-core/propr/propr/templates/propr.R b/modules/nf-core/propr/propr/templates/propr.R new file mode 100644 index 00000000..1f8c6769 --- /dev/null +++ b/modules/nf-core/propr/propr/templates/propr.R @@ -0,0 +1,452 @@ +#!/usr/bin/env Rscript + + +################################################ +################################################ +## Functions ## +################################################ +################################################ + +#' Parse out options from a string without recourse to optparse +#' +#' @param x Long-form argument list like --opt1 val1 --opt2 val2 +#' +#' @return named list of options and values similar to optparse + +parse_args <- function(x){ + args_list <- unlist(strsplit(x, ' ?--')[[1]])[-1] + args_vals <- lapply(args_list, function(x) scan(text=x, what='character', quiet = TRUE)) + + # Ensure the option vectors are length 2 (key/ value) to catch empty ones + args_vals <- lapply(args_vals, function(z){ length(z) <- 2; z}) + + parsed_args <- structure(lapply(args_vals, function(x) x[2]), names = lapply(args_vals, function(x) x[1])) + parsed_args[! is.na(parsed_args)] +} + +#' Flexibly read CSV or TSV files +#' +#' @param file Input file +#' @param header Boolean. TRUE if first row is header. False without header. +#' @param row.names The first column is used as row names by default. +#' Otherwise, give another number. Or use NULL when no row.names are present. +#' +#' @return output Data frame +read_delim_flexible <- function(file, header = TRUE, row.names = 1, check.names = TRUE){ + + ext <- tolower(tail(strsplit(basename(file), split = "\\\\.")[[1]], 1)) + + if (ext == "tsv" || ext == "txt") { + separator <- "\\t" + } else if (ext == "csv") { + separator <- "," + } else { + stop(paste("Unknown separator for", ext)) + } + + mat <- read.delim( + file, + sep = separator, + header = header, + row.names = row.names, + check.names = check.names + ) + + if ( (row.names == 'gene_id') & ('gene_name' %in% colnames(mat)) ){ + mat <- mat[, -which(colnames(mat) == 'gene_name')] + } else if ( (row.names == 'gene_name') & ('gene_id' %in% colnames(mat)) ){ + mat <- mat[, -which(colnames(mat) == 'gene_id')] + } + + return(mat) +} + +#' Check if a variable can be numeric or not +#' +#' @param x Input variable +#' @return True if it can be numeric, False otherwise +can_be_numeric <- function(x) { + stopifnot(is.atomic(x) || is.list(x)) # check if x is a vector + numNAs <- sum(is.na(x)) + numNAs_new <- suppressWarnings(sum(is.na(as.numeric(x)))) + return(numNAs_new == numNAs) +} + +#' Set the proper reference gene index. +#' This should be used for alr transformation only. +#' +#' @param ivar Reference variable given by user. +#' If it is 'null', then set the last column as reference (default). +#' Otherwise, it should refer to either gene name or gene index. +#' If the gene name is given, find its index. +#' @param mat Data matrix, with genes as columns +#' +#' @return The reference gene index +set_reference <- function(ivar, mat){ + if (is.na(ivar)){ + ivar <- ncol(mat) + } else { + isnumeric <- can_be_numeric(ivar) + if (!isnumeric){ + genes <- colnames(mat) + ivar <- which(genes == ivar) + } + ivar <- as.integer(ivar) + } + return(ivar) +} + +#' Set the appropiate range for the sequence of cutoffs used in updateCutoffs. +#' Adjusts the interval to the different metrics. +#' +#' @param object propr object. Output from propr function. +#' +#' @return sequence of cutoff values. +seqCutoff <- function(object){ + matrix <- getMatrix(object) + matrix[matrix <= 0] <- NA + diag(matrix) <- NA + min_cutoff <- round(min(matrix, na.rm = TRUE),3) + max_cutoff <- round(max(matrix, na.rm = TRUE),3) + step_cutoff <- (max_cutoff - min_cutoff)/ 20 + seq_cutoff <- seq(min_cutoff, max_cutoff, step_cutoff) + return(seq_cutoff) +} + +#' Extract the proportionality cutoff for a specified FDR value. +#' Gene pairs with a proportionality value higher than the extracted cutoff will be considered significantly proportional. +#' +#' @param object propr object. Output from propr function. updateCutoffs function should be applied to the object previous to valCutoff. +#' @param fdrVal FDR value to extract the cutoff for. Per default 0.05 +#' @param metric Metric used to calculate the proportionality values. Options are 'cor', 'rho', 'phi', 'phs', 'vlr', 'pcor', 'pcor.shrink', 'pcor.bshrink' +#' +#' @return cutoff value. Proportionality values higher than this cutoff are considered significant. +# valCutoff <- function(object, metric, fdrVal = 0.05){ +# fdr_df <- object@fdr +# print(fdr_df) +# metric_up <- c("rho", "cor", "pcor", "pcor.shrink", "pcor.bshrink") +# if (prod(dim(fdr_df) == 0)){ +# warning("Please run updateCutoff on propr first") +# }else{ +# fdr_vals <- fdr_df\$FDR +# if (any(is.na(fdr_vals))){ +# stop("FDR not defined. This metric is not appropiate for the given dataset") +# } +# threshold <- any(fdr_vals <= fdrVal) +# if (metric %in% metric_up){ +# if (threshold){ +# fdr_threshold <- fdr_vals[which.max(fdr_vals <= fdrVal)] +# }else{ +# warning("FDR is higher than the specified threshold for all proportionality values. Using the lowest fdr instead") +# fdr_threshold <- fdr_vals[length(fdr_vals)] +# } +# }else{ +# if (threshold){ +# fdr_threshold <- fdr_vals[which.min(fdr_vals <= fdrVal) - 1] +# }else{ +# warning("FDR is higher than the specified threshold for all proportionality values. Using the lowest fdr instead") +# fdr_threshold <- fdr_vals[1] +# } +# } +# cutoff <- fdr_df\$cutoff[fdr_df\$FDR == fdr_threshold] +# } +# return(cutoff) +# } + + +valCutoff <- function(object, metric, fdrVal = 0.05){ + fdr_df <- object@fdr + print(fdr_df) + # metric_up <- c("rho", "cor", "pcor", "pcor.shrink", "pcor.bshrink") + + if (prod(dim(fdr_df) == 0)){ + warning("Please run updateCutoff on propr first") + }else{ + fdr_vals <- fdr_df\$FDR + if(any(!is.na(fdr_vals))){ # if there is some defined value, continue, else out of range + if(any(fdr_vals <= fdrVal)){ # if there is some value that is belowe the FDR threshold, + fdr_threshold <- fdr_vals[which.max(fdr_vals <= fdrVal)] #choose the highest FDR that is lower than the threshold, else choose the lowest + }else{ + warning("FDR is higher than the specified threshold for all proportionality values. Using the lowest fdr instead") + fdr_threshold <- min(fdr_vals, na.rm = TRUE) + } + cutoff <- fdr_df\$cutoff[which(fdr_df\$FDR == fdr_threshold)] #select the corresponding cutoff value for the FDR + print(cutoff) + }else{ + stop("FDR not defined. This metric is not appropiate for the given dataset") + } + return(cutoff) + } +} + + +#' Convert a proportionality matrix to an adjacency matrix based on a threshold. +#' +#' @param matrix proportionality matrix. Can be extracted from propr object with getMatrix(). +#' @param cutoff Significant proportionality value extracted from valCutoff function. +#' +#' @return Adjacency matrix. Gene pairs with a proportionality value higher than the threshold will have 1, otherwise 0. +convert_to_adjacency <- function(matrix, cutoff, metric) { + if (metric == 'cor' || metric == 'rho' || metric == 'pcor' || metric == 'pcor.shrink' || metric == 'pcor.bshrink'){ + adjacency <- ifelse(matrix > cutoff, 1, 0) + } else { + adjacency <- ifelse(matrix < cutoff, 1, 0) + } + return(adjacency) +} + +################################################ +################################################ +## Parse arguments ## +################################################ +################################################ + +opt <- list( + count = '$count', + prefix = ifelse('$task.ext.prefix' == 'null', '$meta.pathway_name', '$task.ext.prefix'), + transformation = 'clr', + reference = NA, + alpha = NA, + metric = 'pcor.bshrink', + permutation = 0, + cutoff_min = NA, + cutoff_max = NA, + cutoff_interval = NA, + ncores = as.integer('$task.cpus'), + features_id_col = 'gene_id', + fixseed = FALSE, + adjacency = FALSE, + fdrVal = 0.05 +) +opt_types <- list( + count = 'character', + prefix = 'character', + transformation = 'character', + reference = 'character', + alpha = 'numeric', + metric = 'character', + permutation = 'numeric', + cutoff_min = 'numeric', + cutoff_max = 'numeric', + cutoff_interval = 'numeric', + ncores = 'numeric', + features_id_col = 'character', + fixseed = 'logical', + adjacency = 'logical', + fdrVal = 'numeric' +) + +# Apply parameter overrides +args_opt <- parse_args('$task.ext.args') + +for ( ao in names(args_opt)){ + if (! ao %in% names(opt)){ + stop(paste("Invalid option:", ao)) + } else { + + # Preserve classes from defaults where possible + if (! is.null(opt[[ao]])){ + args_opt[[ao]] <- as(args_opt[[ao]], opt_types[[ao]]) + } + # set NA + if (args_opt[[ao]] %in% c('NA', NA, 'null')){ + args_opt[[ao]] <- NA + } + opt[[ao]] <- args_opt[[ao]] + } +} + +# Check if required parameters have been provided +required_opts <- c('count') +missing <- required_opts[unlist(lapply(opt[required_opts], is.null)) | ! required_opts %in% names(opt)] +if (length(missing) > 0){ + stop(paste("Missing required options:", paste(missing, collapse=', '))) +} + +# Check file inputs are valid +for (file_input in c('count')){ + if (is.null(opt[[file_input]])) { + stop(paste("Please provide", file_input), call. = FALSE) + } + if (! file.exists(opt[[file_input]])){ + stop(paste0('Value of ', file_input, ': ', opt[[file_input]], ' is not a valid file')) + } +} + +# check parameters +if (!opt\$metric %in% c('rho', 'phi', 'phs', 'cor', 'vlr', 'pcor', 'pcor.shrink', 'pcor.bshrink')) { + stop('Please make sure you provided the correct metric') +} +if (opt\$metric == 'pcor.bshrink'){ + if (!is.na(opt\$alpha)) stop('Box-cox transformation is not implemented for pcor.bshrink yet.') + if (!opt\$transformation %in% c('clr', 'alr')) stop('Please make sure you provided the correct transformation: clr or alr') +} else { + if (!opt\$transformation %in% c('clr', 'alr', NA)) stop('Please make sure you provided the correct transformation: clr or alr. Or set NA if you dont want to transform the data.') + if (is.na(opt\$transformation)) print('Warning: No transformation is required by user. We assume the input count data was already properly transformed.') +} + +################################################ +################################################ +## Finish loading libraries ## +################################################ +################################################ + +library(corpcor) +library(propr) + +################################################ +################################################ +## Perform correlation analysis ## +################################################ +################################################ + +# read matrix +mat <- read_delim_flexible( + opt\$count, + header = TRUE, + row.names = opt\$features_id_col, + check.names = FALSE +) +mat <- t(mat) + +# check zeros +# log transformation should be applied on non-zero data +# otherwise Inf values are generated +if (any(mat == 0)) print("Warning: Zeros will be replaced by minimun value before logratio analysis") + +# set logratio transformation parameter -> ivar +# if alr, set the index of the reference gene as ivar +# if clr or NA, set same ivar +if (opt\$metric == 'pcor.bshrink'){ + opt\$ivar <- opt\$transformation +}else{ + if (opt\$transformation == 'alr'){ + opt\$ivar <- set_reference(opt\$reference, mat) + gene_name <- colnames(mat)[opt\$ivar] + } else { + opt\$ivar <- opt\$transformation + } +} + +# Compute correlation coefficients +pro <- propr( + mat, + metric = opt\$metric, + ivar = opt\$ivar, + alpha = opt\$alpha, + p = opt\$permutation, + fixseed = opt\$fixseed +) + +# update FDR by permutation, if required + +if (opt\$permutation > 0) { + cutoff <- seq( + opt\$cutoff_min, + opt\$cutoff_max, + opt\$cutoff_interval + ) + if (is.na(opt\$cutoff_min) || is.na(opt\$cutoff_max) || is.na(opt\$cutoff_interval)) { + warning("cutoff values were not provided. Using the default cutoff values.") + cutoff <- seqCutoff(pro) + } + m <- getMatrix(pro) + diag(m) <- NA + print((opt\$cutoff_max - opt\$cutoff_min)/2 + opt\$cutoff_min) + print(max(m, na.rm = TRUE)) + if ((opt\$cutoff_max - opt\$cutoff_min)/2 + opt\$cutoff_min > max(m, na.rm = TRUE)) { + warning("The provided cutoff values are out of range. Using the default cutoff values.") + cutoff <- seqCutoff(pro) + } + pro <- updateCutoffs(pro, cutoff=cutoff, ncores=opt\$ncores) +} + +# calculate cutoff and adjacency matrix, if required + +if (opt\$adjacency == TRUE) { + cutoff <- valCutoff(pro, opt\$metric, opt\$fdrVal) + matrix <- getMatrix(pro) + adj <- convert_to_adjacency(matrix, cutoff, opt\$metric) +} + +################################################ +################################################ +## Generate outputs ## +################################################ +################################################ + +saveRDS( + pro, + file = paste0(opt\$prefix, '.propr.rds') +) + +write.table( + round(pro@matrix, 8), # round matrix decimals to avoid floating point inconsistencies + file = paste0(opt\$prefix, '.propr.tsv'), + col.names = TRUE, + row.names = TRUE, + sep = '\t', + quote = FALSE +) + +if (opt\$permutation > 0) { + write.table( + pro@fdr, + file = paste0(opt\$prefix, '.fdr.tsv'), + col.names = TRUE, + row.names = FALSE, + sep = '\t', + quote = FALSE + ) +} + +if (opt\$adjacency == TRUE) { + write.table( + adj, + file = paste0(opt\$prefix, '.adj.csv'), + col.names = TRUE, + row.names = TRUE, + sep = ',', + quote = FALSE + ) +} + +################################################ +################################################ +## WARNINGS ## +################################################ +################################################ + +sink(paste0(opt\$prefix, ".warnings.log")) +print(warnings()) +sink() + +################################################ +################################################ +## R SESSION INFO ## +################################################ +################################################ + +sink(paste0(opt\$prefix, ".R_sessionInfo.log")) +print(sessionInfo()) +sink() + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +propr.version <- as.character(packageVersion('propr')) + +writeLines( + c( + '"${task.process}":', + paste(' r-propr:', propr.version) + ), +'versions.yml') + +################################################ +################################################ +################################################ +################################################ diff --git a/modules/nf-core/propr/propr/tests/adjacency.config b/modules/nf-core/propr/propr/tests/adjacency.config new file mode 100644 index 00000000..cc0b3894 --- /dev/null +++ b/modules/nf-core/propr/propr/tests/adjacency.config @@ -0,0 +1,3 @@ +process { + ext.args = {"--metric rho --permutation 10 --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.1 --fixseed true --adjacency true"} +} diff --git a/modules/nf-core/propr/propr/tests/adjacency_pcor.config b/modules/nf-core/propr/propr/tests/adjacency_pcor.config new file mode 100644 index 00000000..0dda6b73 --- /dev/null +++ b/modules/nf-core/propr/propr/tests/adjacency_pcor.config @@ -0,0 +1,3 @@ +process { + ext.args = {"--metric pcor.bshrink --permutation 10 --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.1 --fixseed true --adjacency true"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propr/tests/adjacency_phs.config b/modules/nf-core/propr/propr/tests/adjacency_phs.config new file mode 100644 index 00000000..923570b4 --- /dev/null +++ b/modules/nf-core/propr/propr/tests/adjacency_phs.config @@ -0,0 +1,3 @@ +process { + ext.args = {"--metric phs --permutation 10 --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.1 --fixseed true --adjacency true"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propr/tests/adjacency_rho.config b/modules/nf-core/propr/propr/tests/adjacency_rho.config new file mode 100644 index 00000000..cc0b3894 --- /dev/null +++ b/modules/nf-core/propr/propr/tests/adjacency_rho.config @@ -0,0 +1,3 @@ +process { + ext.args = {"--metric rho --permutation 10 --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.1 --fixseed true --adjacency true"} +} diff --git a/modules/nf-core/propr/propr/tests/alr_pcorbshrink.config b/modules/nf-core/propr/propr/tests/alr_pcorbshrink.config new file mode 100644 index 00000000..c0c3b211 --- /dev/null +++ b/modules/nf-core/propr/propr/tests/alr_pcorbshrink.config @@ -0,0 +1,3 @@ +process { + ext.args = {"--transformation alr --metric pcor.bshrink --permutation 10 --cutoff_min 0.001 --cutoff_max 0.01 --cutoff_interval 0.001 --fixseed true"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propr/tests/clr_pcor.config b/modules/nf-core/propr/propr/tests/clr_pcor.config new file mode 100644 index 00000000..2e6d1b19 --- /dev/null +++ b/modules/nf-core/propr/propr/tests/clr_pcor.config @@ -0,0 +1,3 @@ +process { + ext.args = {"--transformation clr --metric pcor --permutation 10 --cutoff_min 0.001 --cutoff_max 0.01 --cutoff_interval 0.001 --fixseed true"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propr/tests/clr_pcorbshrink.config b/modules/nf-core/propr/propr/tests/clr_pcorbshrink.config new file mode 100644 index 00000000..435440c8 --- /dev/null +++ b/modules/nf-core/propr/propr/tests/clr_pcorbshrink.config @@ -0,0 +1,3 @@ +process { + ext.args = {"--transformation clr --metric pcor.bshrink --permutation 10 --cutoff_min 0.001 --cutoff_max 0.01 --cutoff_interval 0.001 --fixseed true"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propr/tests/clr_rho.config b/modules/nf-core/propr/propr/tests/clr_rho.config new file mode 100644 index 00000000..6b32ac27 --- /dev/null +++ b/modules/nf-core/propr/propr/tests/clr_rho.config @@ -0,0 +1,3 @@ +process { + ext.args = {"--transformation clr --metric rho --permutation 10 --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.1 --fixseed true"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propr/tests/clr_rho_alpha.config b/modules/nf-core/propr/propr/tests/clr_rho_alpha.config new file mode 100644 index 00000000..7f151a80 --- /dev/null +++ b/modules/nf-core/propr/propr/tests/clr_rho_alpha.config @@ -0,0 +1,3 @@ +process { + ext.args = {"--transformation alr --alpha 0.2 --metric rho --permutation 10 --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.1 --fixseed true"} +} \ No newline at end of file diff --git a/modules/nf-core/propr/propr/tests/main.nf.test b/modules/nf-core/propr/propr/tests/main.nf.test new file mode 100644 index 00000000..e262d2cf --- /dev/null +++ b/modules/nf-core/propr/propr/tests/main.nf.test @@ -0,0 +1,240 @@ +nextflow_process { + + name "Test Process PROPR_PROPR" + script "../main.nf" + process "PROPR_PROPR" + + tag "modules" + tag "modules_nfcore" + tag "propr" + tag "propr/propr" + + test("Test propr/propr using default options") { + + tag "default" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + //file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true) + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.matrix).match("Test propr/propr using default options - matrix") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("Test propr/propr while running clr+pcor.bshrink explicitly") { + + tag "clr_pcorbshrink" + config "./clr_pcorbshrink.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.matrix).match("Test propr/propr while running clr+pcor.bshrink explicitly - matrix")}, + { assert snapshot(process.out.fdr).match("Test propr/propr while running clr+pcor.bshrink explicitly - fdr")} + ) + } + } + + test("Test propr/propr while running alr+pcor.bshrink") { + + tag "alr_pcorbshrink" + config "./alr_pcorbshrink.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true) + ] + """ + } + } + + then { + // TODO also check that the first columns are the same as the above processes + assertAll( + { assert process.success }, + { assert snapshot(process.out.matrix).match("Test propr/propr while running alr+pcor.bshrink - matrix") }, + { assert snapshot(process.out.fdr).match("Test propr/propr while running alr+pcor.bshrink - fdr") } + ) + } + } + + test("Test propr/propr while running clr+rho") { + + tag "clr_rho" + config "./clr_rho.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.matrix).match("Test propr/propr while running clr+rho - matrix") }, + { assert snapshot(process.out.fdr).match("Test propr/propr while running clr+rho - fdr") } + ) + } + } + + test("Test propr/propr while running clr+pcor") { + + tag "clr_pcor" + config "./clr_pcor.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.matrix).match("Test propr/propr while running clr+pcor - matrix") }, + { assert snapshot(process.out.fdr).match("Test propr/propr while running clr+pcor - fdr") } + ) + } + } + + test("Test propr/propr while running clr+rho with boxcox transformation") { + + tag "clr_rho_alpha" + config "./clr_rho_alpha.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.matrix).match("Test propr/propr while running clr+rho with boxcox transformation - matrix") }, + { assert snapshot(process.out.fdr).match("Test propr/propr while running clr+rho with boxcox transformation - fdr") } + ) + } + } + + test("Test propr/propr calculating adjacency_matrix for rho") { + + tag "adjacency_rho" + config "./adjacency_rho.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.matrix).match("Test propr/propr calculating adjacency_matrix for rho - matrix") }, + { assert snapshot(process.out.fdr).match("Test propr/propr calculating adjacency_matrix for rho - fdr") }, + { assert snapshot(process.out.adj).match("Test propr/propr calculating adjacency_matrix for rho - adj") } + ) + } + } + + test("Test propr/propr calculating adjacency_matrix for phs") { + + tag "adjacency_phs" + config "./adjacency_phs.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.matrix).match("Test propr/propr calculating adjacency_matrix for phs - matrix") }, + { assert snapshot(process.out.fdr).match("Test propr/propr calculating adjacency_matrix for phs - fdr") }, + { assert snapshot(process.out.adj).match("Test propr/propr calculating adjacency_matrix for phs - adj") } + ) + } + } + + test("Test propr/propr calculating adjacency_matrix for pcor") { + + tag "adjacency_pcor" + config "./adjacency_pcor.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.matrix).match("Test propr/propr calculating adjacency_matrix for pcor - matrix") }, + { assert snapshot(process.out.fdr).match("Test propr/propr calculating adjacency_matrix for pcor - fdr") }, + { assert snapshot(process.out.adj).match("Test propr/propr calculating adjacency_matrix for pcor - adj") } + ) + } + } +} diff --git a/modules/nf-core/propr/propr/tests/main.nf.test.snap b/modules/nf-core/propr/propr/tests/main.nf.test.snap new file mode 100644 index 00000000..cde969bc --- /dev/null +++ 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"test.propr.tsv:md5,67ba22131ebd747404a3037f922a77f5" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-05T11:23:43.441629" + } +} \ No newline at end of file diff --git a/modules/nf-core/propr/propr/tests/tags.yml b/modules/nf-core/propr/propr/tests/tags.yml new file mode 100644 index 00000000..539706d4 --- /dev/null +++ b/modules/nf-core/propr/propr/tests/tags.yml @@ -0,0 +1,2 @@ +propr/propr: + - "modules/nf-core/propr/propr/**" From 708c4db047398e9188f7ab7ac8e3b56f2653570b Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 10:53:14 +0200 Subject: [PATCH 02/15] add functional subworkflows into subworkflows/local --- subworkflows/local/correlation/main.nf | 48 ++++++++++++ subworkflows/local/differential/main.nf | 33 +++++++++ subworkflows/local/enrichment/main.nf | 46 ++++++++++++ subworkflows/local/experimental/main.nf | 73 +++++++++++++++++++ subworkflows/local/variable_selection/main.nf | 40 ++++++++++ 5 files changed, 240 insertions(+) create mode 100644 subworkflows/local/correlation/main.nf create mode 100644 subworkflows/local/differential/main.nf create mode 100644 subworkflows/local/enrichment/main.nf create mode 100644 subworkflows/local/experimental/main.nf create mode 100644 subworkflows/local/variable_selection/main.nf diff --git a/subworkflows/local/correlation/main.nf b/subworkflows/local/correlation/main.nf new file mode 100644 index 00000000..5aaad2e2 --- /dev/null +++ b/subworkflows/local/correlation/main.nf @@ -0,0 +1,48 @@ + +// include nf-core modules +include {PROPR_PROPR as PROPR} from "../../modules/nf-core/propr/propr/main.nf" + + +workflow CORRELATION { + take: + ch_counts + ch_tools + ch_counts_filtered + + main: + ch_counts + .combine(ch_tools) + .map { + metacounts, counts, metatools -> + [ metacounts+metatools, counts ] + } + .branch { + propr: it[0]["cor_method"] == "propr" + } + .set { ch_counts_cor } + + // Hacer un branch del channel para coger las counts normales cuando no hay variable selection + + ch_counts_cor.propr + .branch{ + no_sel: it[0]["sel_method"] == null + sel: it[0]["sel_method"] != null + } + .set { ch_counts_selection } + + //ch_counts_selection.no_sel.view() + //ch_counts_filtered.view() + + ch_propr = ch_counts_filtered.mix(ch_counts_selection.no_sel) + //ch_propr.view() + + PROPR(ch_propr) + ch_matrix = PROPR.out.matrix + ch_adjacency = PROPR.out.adj + + + emit: + matrix = ch_matrix + adjacency = ch_adjacency + +} \ No newline at end of file diff --git a/subworkflows/local/differential/main.nf b/subworkflows/local/differential/main.nf new file mode 100644 index 00000000..15948b9c --- /dev/null +++ b/subworkflows/local/differential/main.nf @@ -0,0 +1,33 @@ +// include modules +include {PROPR_PROPD as PROPD} from "../../modules/nf-core/propr/propd/main.nf" + + +workflow DIFFERENTIAL { + take: + ch_counts + ch_tools + ch_samplesheet + + main: + ch_counts + .combine(ch_tools) + .map { + metacounts, counts, meta -> + [ metacounts+meta, counts ] + } + //.view() + .branch { + propd: it[0]["diff_method"] == "propd" + deseq2: it[0]["diff_method"] == "deseq2" + } + .set { ch_counts_tools } + + PROPD(ch_counts_tools.propd, ch_samplesheet) + ch_results = PROPD.out.results + ch_adjacency = PROPD.out.adj + + emit: + results = ch_results + adjacency = ch_adjacency + +} \ No newline at end of file diff --git a/subworkflows/local/enrichment/main.nf b/subworkflows/local/enrichment/main.nf new file mode 100644 index 00000000..442014a3 --- /dev/null +++ b/subworkflows/local/enrichment/main.nf @@ -0,0 +1,46 @@ +// include modules + +include { PROPR_GREA as GREA_DIFF } from "../../modules/nf-core/propr/grea/main.nf" +include { PROPR_GREA as GREA_COR } from "../../modules/nf-core/propr/grea/main.nf" +include { MYGENE } from "../../modules/nf-core/mygene/main.nf" + + +workflow ENRICHMENT { + take: + ch_diff_adjacency + ch_cor_adjacency + ch_counts + + + main: + + MYGENE(ch_counts) + ch_gmt = MYGENE.out.gmt + + + ch_diff_adjacency + .branch { + grea: it[0]["enr_diff_method"] == "grea" + gsea: it[0]["enr_diff_method"] == "gsea" + } + .set { ch_diff_grea } + + GREA_DIFF(ch_diff_grea.grea, ch_gmt.collect()) + ch_enriched_diff = GREA_DIFF.out.enrichedGO + + ch_cor_adjacency + .branch { + grea: it[0]["enr_cor_method"] == "grea" } + .set { ch_cor_grea } + + ch_cor_grea.grea.view() + ch_diff_grea.grea.view() + + GREA_COR(ch_cor_grea.grea, ch_gmt.collect()) + ch_enriched_cor = GREA_COR.out.enrichedGO + + + emit: + enriched_diff = ch_enriched_diff + enriched_cor = ch_enriched_cor +} \ No newline at end of file diff --git a/subworkflows/local/experimental/main.nf b/subworkflows/local/experimental/main.nf new file mode 100644 index 00000000..6e26eb6d --- /dev/null +++ b/subworkflows/local/experimental/main.nf @@ -0,0 +1,73 @@ +// include subworkflows + +include { CORRELATION } from '../correlation/main.nf' +include { DIFFERENTIAL } from '../differential/main.nf' +include { VARIABLE_SELECTION } from '../variable_selection/main.nf' +include { ENRICHMENT } from '../enrichment/main.nf' + + +workflow EXPERIMENTAL { + take: + ch_samples_and_matrix // [meta, samplesheet, matrix] que viene de differentialabundance + ch_tools + + + main: + // Dividir el ch_samples_and_matrix en un channel de samplesheet y otro de matrix (PROPD los coge por separado) + ch_samples_and_matrix + .map { + meta, samplesheet, counts -> + [ meta, samplesheet ] + } + .set { ch_samplesheet } + + ch_samples_and_matrix + .map { + meta, samplesheet, counts -> + [ meta, counts ] + } + .set { ch_counts } + // ch_counts.view() + + ch_counts + .combine(ch_tools) + .map { + metacounts, counts, metatools -> + [ metacounts+metatools, counts ] + } + .set { ch_counts_tools } + + // Perform CODA analysis + ch_out = Channel.empty() + + // Perform differential analysis + + DIFFERENTIAL(ch_counts, ch_tools, ch_samplesheet.collect()) + ch_diff_results = DIFFERENTIAL.out.results + ch_diff_adjacency = DIFFERENTIAL.out.adjacency + + // Perform variable selection + ch_counts_filtered = VARIABLE_SELECTION(ch_diff_adjacency, ch_counts) + + //VARIABLE_SELECTION.out.count.view() + + // Perform correlation analysis + CORRELATION(ch_counts, ch_tools, ch_counts_filtered) + ch_matrix = CORRELATION.out.matrix + ch_cor_adjacency = CORRELATION.out.adjacency + ch_out.mix(ch_matrix) + + //ch_diff_adjacency.view() + //ch_cor_adjacency.view() + + // Perform enrichment analysis + ENRICHMENT(ch_diff_adjacency, ch_cor_adjacency, ch_counts) + ch_enriched_cor = ENRICHMENT.out.enriched_cor + ch_enriched_diff = ENRICHMENT.out.enriched_diff + + ch_out.mix(ch_enriched_diff, ch_enriched_cor) + + + emit: + output = ch_out +} \ No newline at end of file diff --git a/subworkflows/local/variable_selection/main.nf b/subworkflows/local/variable_selection/main.nf new file mode 100644 index 00000000..d7a176c8 --- /dev/null +++ b/subworkflows/local/variable_selection/main.nf @@ -0,0 +1,40 @@ +// include modules +include { FILTERVAR } from "../../modules/local/filtervar/main.nf" + +workflow VARIABLE_SELECTION { + take: + ch_adj//meta_tools, adj + ch_counts //meta_id, counts + + + main: + ch_counts + .map { + metacounts, counts -> + [counts] + } + .combine(ch_adj) + //.view() + .map{ + counts, meta, adj -> + [ meta, counts, adj] + } + //.view() + .branch { + filtervar: it[0]["sel_method"] == "filtervar" + deseqfilter: it[0]["sel_method"] == "deseqfilter" + } + .set { ch_counts_adj_sel } + + //ch_counts_adj_sel.nofilter.view() + + + FILTERVAR(ch_counts_adj_sel.filtervar) + + ch_counts_cor = FILTERVAR.out.count + //ch_counts_cor.view() + + + emit: + count = ch_counts_cor +} \ No newline at end of file From 4a76cefec21ec6b4784218e305c275e962733ad3 Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 14:18:19 +0200 Subject: [PATCH 03/15] add schema_tools and tools_samplesheet to assets --- assets/schema_tools.json | 61 ++++++++++++++++++++++++++++++++++++ assets/tools_samplesheet.csv | 6 ++++ 2 files changed, 67 insertions(+) create mode 100644 assets/schema_tools.json create mode 100644 assets/tools_samplesheet.csv diff --git a/assets/schema_tools.json b/assets/schema_tools.json new file mode 100644 index 00000000..4119c58e --- /dev/null +++ b/assets/schema_tools.json @@ -0,0 +1,61 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "title": "nf-core/differentialabundance - params.tools schema", + "description": "Schema for the file provided with params.tools", + "type": "array", + "items": { + "type": "object", + "properties": { + "pathway_name": { + "type": "string", + "meta": ["pathway_name"] + }, + "diff_method": { + "type": "string", + "errorMessage": "choose propd, DESeq2 or none", + "meta": ["diff_method"] + }, + "args_diff": { + "type": "string", + "meta": ["args_diff"] + }, + "enr_diff_method": { + "type": "string", + "meta": ["enr_diff_method"], + "errorMessage": "choose grea, gsea or none" + }, + "args_enr_diff": { + "type": "string", + "meta": ["args_enr_diff"] + }, + "cor_method": { + "type": "string", + "meta": ["cor_method"], + "errorMessage": "choose correlation,proportionality, partial correlation or none" + }, + "args_cor": { + "type": "string", + "meta": ["args_cor"] + }, + "enr_cor_method": { + "type": "string", + "meta": ["enr_cor_method"], + "errorMessage": "choose grea or none" + }, + "args_enr_cor": { + "type": "string", + "meta": ["args_enr_cor"] + }, + "sel_method":{ + "type": "string", + "meta": ["sel_method"], + "errorMessage": "choose filtervar or none" + }, + "args_sel": { + "type": "string", + "meta": ["args_sel"] + } + }, + "required": [] + } +} diff --git a/assets/tools_samplesheet.csv b/assets/tools_samplesheet.csv new file mode 100644 index 00000000..f6147f34 --- /dev/null +++ b/assets/tools_samplesheet.csv @@ -0,0 +1,6 @@ +pathway_name,diff_method,args_diff,enr_diff_method,args_enr_diff,cor_method,args_cor,enr_cor_method,args_enr_cor,sel_method,args_sel +diff_prop,propd, --adjacency true --permutation 100 --fixseed true, , ,,, , ,, +filtered_pcor,propd, --adjacency true --permutation 100 --fixseed true, , ,propr, --permutation 10 --adjacency true --cutoff_min 0.005 --cutoff_max 0.5 --cutoff_interval 0.01 --metric pcor.bshrink, , , filtervar, +prop,, , , ,propr, --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --fixseed true --metric rho --permutation 100 --adjacency true, , , , +diff_grea,propd,--group_col fase --adjacency true --permutation 10,grea, --permutation 10, , , , ,, +deseq2,deseq2,,gsea,,,,,,, \ No newline at end of file From 93ae92db8f3190356d5ab7cbe7700d8f84109447 Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 14:25:33 +0200 Subject: [PATCH 04/15] add crg.config and modules.config (as modules_coda) to conf --- conf/crg.config | 41 ++++++++++++++++++++++++++++++++++++ conf/modules_coda.config | 45 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 conf/crg.config create mode 100644 conf/modules_coda.config diff --git a/conf/crg.config b/conf/crg.config new file mode 100644 index 00000000..07da3727 --- /dev/null +++ b/conf/crg.config @@ -0,0 +1,41 @@ +params { + config_profile_name = 'CRG profile' + config_profile_description = 'Configuration to run on CRG cluster' + + max_cpus = 64 + max_memory = 100.GB + max_time = 48.h +} + + +process { + executor = 'crg' + //maxRetries = params.max_retries + //errorStrategy = params.err_start + + withLabel:process_low { + queue = 'cn-el7,short-centos79' + cpus = { check_max( 2 , 'cpus' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } + } + withLabel:process_medium{ + queue = 'cn-el7,short-centos79' + cpus = { check_max( 6 , 'cpus' ) } + memory = { check_max( 36.GB * task.attempt, 'memory' ) } + time = { check_max( 8.h * task.attempt, 'time' ) } + } + withLabel:process_high { + queue = 'cn-el7,long-centos79' + cpus = { check_max( 12 , 'cpus' ) } + memory = { check_max( 56.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } + + } +} + + +singularity { + enabled = true + cacheDir = 'singularity_cache' +} \ No newline at end of file diff --git a/conf/modules_coda.config b/conf/modules_coda.config new file mode 100644 index 00000000..a783c00e --- /dev/null +++ b/conf/modules_coda.config @@ -0,0 +1,45 @@ +process { + withName: "PROPR"{ + ext.args = { "${meta.args_cor}" == "null" ? '' : "${meta.args_cor}" } + publishDir = [ + path: { "${params.outdir}/correlation_analysis/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: "PROPD"{ + ext.args = { "${meta.args_diff}" == "null" ? '' : "${meta.args_diff}" } + publishDir = [ + path: { "${params.outdir}/differential_analysis/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: "FILTERVAR"{ + ext.args = { "${meta.args_cor}" == "null" ? '' : "${meta.args_cor}" } + publishDir = [ + path: { "${params.outdir}/variable_selection/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: "GREA_DIFF"{ + ext.args = { "${meta.args_enr_diff}" == "null" ? '' : "${meta.args_enr_diff}" } + publishDir = [ + path: { "${params.outdir}/enrichment_differential/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: "GREA_COR"{ + ext.args = { "${meta.args_enr_cor}" == "null" ? '' : "${meta.args_enr_cor}" } + publishDir = [ + path: { "${params.outdir}/enrichment_correlation/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file From da30859515965628e461ab6062fe721eefe8bfaf Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 14:35:32 +0200 Subject: [PATCH 05/15] add main.nf as main_coda.nf --- main_coda.nf | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 main_coda.nf diff --git a/main_coda.nf b/main_coda.nf new file mode 100644 index 00000000..6a62390e --- /dev/null +++ b/main_coda.nf @@ -0,0 +1,40 @@ +// include { PROPR_PROPR } from '../../../modules/nf-core/propr/propr/main' +// include { PROPR_PROPD } from '../../../modules/nf-core/propr/propd/main' +// include { PROPR_GREA } from '../../../modules/nf-core/propr/grea/main' +// include { MYGENE } from '../../../modules/nf-core/mygene/main' +include { EXPERIMENTAL } from './subworkflows/experimental/main.nf' +include { fromSamplesheet } from 'plugin/nf-validation' + + +// These are local files from my Bachelor Thesis project, I am creating the ch_samples_and_matrix +// manually for testing but it should be be provided by the processing section of nf-core/differentialabundance +Counts_ch = Channel.fromPath("../YMC/counts_sin0.csv") + +Sample_ch = Channel.fromPath("../YMC/samplesheet_RCvsOX.csv") + .map{ it -> [[id: 'YMC'], it]} + +ch_samples_and_matrix = Sample_ch.combine(Counts_ch) + +// Convert the samplesheet.csv in a channel with the proper format +ch_tools = Channel.fromSamplesheet('tools') + + +// TO DO: This should be modified to run one path per default, not all +if (params.pathway == "all") { + ch_tools + .set{ ch_tools_single } +} else { + ch_tools + .filter{ + it[0]["pathway_name"] == params.pathway // TO DO: change pathway to path also in the tools_samplesheet file + } + //.view() + .set{ ch_tools_single } +} +ch_tools_single.view() + +workflow { + EXPERIMENTAL(ch_samples_and_matrix, ch_tools_single) + EXPERIMENTAL.out.output.view() +} + From 748778915726732f73c9212b6858b47077bf1552 Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 14:43:34 +0200 Subject: [PATCH 06/15] add nextflow.config and nextflow schema as nextflow_coda and nextflow_schema_coda --- nextflow_coda.config | 55 +++++++++++++++++++++++++++++++++++++++ nextflow_schema_coda.json | 25 ++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 nextflow_coda.config create mode 100644 nextflow_schema_coda.json diff --git a/nextflow_coda.config b/nextflow_coda.config new file mode 100644 index 00000000..3ed7f425 --- /dev/null +++ b/nextflow_coda.config @@ -0,0 +1,55 @@ +//parametros generales, para el usuario (que se pueden arrancar poniendo los flags como el command line) + +params.tools = "./assets/tools_samplesheet.csv" +params.outdir = "../results_pipeline" +params.validationSkipDuplicateCheck = true +params.publish_dir_mode = 'copy' +params.pathway = 'all' +//params.maxRetries = 0 +includeConfig 'conf/modules.config' // now it should refer to modules_coda.config + + + +profiles { + debug { + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + process.debug = true + cleanup = false + nextflow.enable.configProcessNamesValidation = true + } + crg { includeConfig "conf/crg.config" } +} + +// Function to ensure that resource requirements don't go beyond +// a maximum limit +def check_max(obj, type) { + if (type == 'memory') { + try { + if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) + return params.max_memory as nextflow.util.MemoryUnit + else + return obj + } catch (all) { + println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'time') { + try { + if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) + return params.max_time as nextflow.util.Duration + else + return obj + } catch (all) { + println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'cpus') { + try { + return Math.min( obj, params.max_cpus as int ) + } catch (all) { + println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" + return obj + } + } +} \ No newline at end of file diff --git a/nextflow_schema_coda.json b/nextflow_schema_coda.json new file mode 100644 index 00000000..76b4f1dd --- /dev/null +++ b/nextflow_schema_coda.json @@ -0,0 +1,25 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "title": "nf-core/testpipeline pipeline parameters", + "description": "this is a test", + "type": "object", + "definitions": { + "tools_options": { + "title": "Tools options", + "type": "object", + "description": "Define where the pipeline should find input data", + "required": ["tools"], + "properties": { + "tools": { + "type": "string", + "format": "file-path", + "mimetype": "text/csv", + "schema": "assets/schema_tools.json", + "pattern": "^\\S+\\.(csv|tsv|yaml)$", + "description": "Path to comma-separated file containing samplesheet", + "help_text": "this is just a test" + } + } + } + } +} \ No newline at end of file From a91626b78b67dbd42a5bd86204137e8c8be86762 Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 15:00:33 +0200 Subject: [PATCH 07/15] add YMC counts and samplesheet to help for testing --- test_data/YMC/counts_sin0.csv | 5840 ++++++++++++++++++++++++++ test_data/YMC/samplesheet_RCvsOX.csv | 10 + 2 files changed, 5850 insertions(+) create mode 100644 test_data/YMC/counts_sin0.csv create mode 100644 test_data/YMC/samplesheet_RCvsOX.csv diff --git a/test_data/YMC/counts_sin0.csv b/test_data/YMC/counts_sin0.csv new file mode 100644 index 00000000..58ea62af --- /dev/null +++ b/test_data/YMC/counts_sin0.csv @@ -0,0 +1,5840 @@ +"gene_id","Time.1","Time.2","Time.3","Time.4","Time.5","Time.13","Time.14","Time.15","Time.16" +"YAL068C",57,52,82,93,66,12,33,34,52 +"YAL063C",82,94,62,69,99,99,64,72,105 +"YAL062W",2280,2753,2819,2270,1033,2942,1535,2444,4300 +"YAL061W",2970,2391,1049,64,170,4379,2215,2849,4953 +"YAL060W",2354,1727,1039,378,578,5618,2218,2790,4385 +"YAL059W",339,534,832,1966,2627,51,185,189,360 +"YAL058W",362,459,447,574,546,229,266,279,491 +"YAL056W",1440,1269,894,233,393,1094,1083,1122,1763 +"YAL055W",266,305,255,61,108,190,246,277,477 +"YAL054C",27781,19019,8956,842,151,65763,49692,34469,45068 +"YAL053W",2027,2120,2779,3995,1796,963,1298,1864,2887 +"YAL051W",738,774,529,417,516,471,515,590,849 +"YAL049C",1752,1677,1138,592,382,1650,1602,1692,2793 +"YAL048C",594,557,428,361,305,434,393,401,619 +"YAL047C",361,393,343,276,335,195,225,222,341 +"YAL046C",212,223,211,170,207,377,201,221,344 +"YAL044W-A",543,477,401,403,350,566,570,599,895 +"YAL044C",1313,1345,1376,1512,1792,1237,1033,1109,1959 +"YAL043C",662,765,740,610,608,421,524,478,781 +"YAL042W",1402,1561,1514,1458,1497,1612,1611,1525,2301 +"YAL041W",874,1009,931,806,780,569,603,541,939 +"YAL040C",461,496,781,1188,1398,268,354,485,527 +"YAL039C",597,784,1003,891,658,1037,770,694,1154 +"YAL038W",58112,51535,41160,35725,15242,7632,8910,23994,59573 +"YAL037C-A",17,15,10,6,9,3,2,7,16 +"YAL037W",136,135,103,97,123,92,104,132,188 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+"YDR217C",822,1003,969,1226,951,352,462,458,797 +"YDR218C",398,343,256,133,97,249,270,329,591 +"YDR219C",704,677,561,396,595,777,662,642,923 +"YDR221W",1089,1206,1061,833,505,630,618,620,1115 +"YDR222W",479,608,655,1360,458,323,286,338,589 +"YDR223W",2071,1674,945,181,151,3189,1625,1769,2950 +"YDR224C",6159,5872,4590,3429,3656,6651,4813,4605,7860 +"YDR225W",5459,4454,3026,2319,2216,6080,5630,6127,10355 +"YDR226W",2504,2659,2460,3640,4991,2439,2051,2474,4039 +"YDR227W",1246,1330,1099,1072,1003,658,853,798,1331 +"YDR228C",858,797,646,652,1180,761,695,723,1122 +"YDR229W",790,852,633,352,356,767,699,788,1231 +"YDR231C",987,1009,719,371,450,1310,1103,1127,1635 +"YDR232W",1797,2122,2631,4237,2517,905,1325,1281,2004 +"YDR233C",3717,3607,3322,3856,4589,1979,2843,2734,4141 +"YDR234W",1779,3256,4590,9017,9837,282,621,614,1262 +"YDR235W",408,437,409,451,587,300,348,301,435 +"YDR236C",397,387,322,248,259,299,314,362,624 +"YDR237W",362,397,402,414,550,1906,496,338,490 +"YDR238C",3134,3406,3145,3394,3035,2634,2465,2275,3435 +"YDR239C",469,509,456,432,461,285,306,307,549 +"YDR240C",308,375,349,375,436,174,203,219,369 +"YDR242W",612,718,538,433,437,330,377,378,695 +"YDR243C",313,404,427,457,266,183,193,188,323 +"YDR244W",1233,1431,936,469,699,2307,1522,1281,1586 +"YDR245W",932,1195,1413,2031,2125,693,865,819,1199 +"YDR246W",548,545,386,166,189,389,448,428,772 +"YDR246W-A",23,14,10,5,9,37,25,22,49 +"YDR247W",724,568,300,85,254,787,706,666,987 +"YDR248C",1110,1382,1235,1071,493,841,738,852,1603 +"YDR249C",149,195,212,277,319,98,91,114,171 +"YDR251W",1078,1084,806,535,855,1182,906,906,1300 +"YDR252W",85,72,78,56,31,84,107,84,134 +"YDR253C",597,746,843,1312,526,255,453,471,775 +"YDR254W",608,502,320,172,283,530,502,453,736 +"YDR255C",855,769,486,154,281,585,567,603,904 +"YDR256C",10753,8212,4002,404,354,43475,29705,19465,22136 +"YDR257C",362,497,541,852,1011,243,320,315,413 +"YDR258C",11660,8819,5236,1133,1254,14785,7934,8183,14886 +"YDR259C",186,236,351,411,306,207,268,187,233 +"YDR260C",350,336,300,343,295,224,277,325,510 +"YDR261C",163,206,198,264,328,304,171,151,237 +"YDR261W-B",43,61,61,19,15,28,18,9,36 +"YDR261C-D",50,55,56,32,54,37,40,39,65 +"YNCD0020W",56,37,23,18,5,27,28,35,55 +"YDR262W",3255,2858,1987,1176,1054,1822,1955,2278,4505 +"YDR263C",114,115,72,54,144,201,131,97,176 +"YDR264C",1497,1675,1562,1190,1215,1105,1203,1288,1835 +"YDR265W",431,470,361,219,283,423,397,392,609 +"YDR266C",465,562,751,1256,1248,255,392,352,512 +"YDR267C",453,515,548,679,717,351,408,403,610 +"YDR268W",133,159,170,170,195,532,159,129,155 +"YDR270W",735,747,646,227,242,762,564,517,847 +"YDR272W",1842,1784,1415,1048,1146,1651,1605,1734,2634 +"YDR273W",158,132,104,97,151,222,140,139,257 +"YDR274C",180,159,114,68,85,200,211,156,236 +"YDR275W",1696,1807,1219,437,630,803,607,815,1964 +"YDR276C",4621,3514,2313,1149,1296,6672,5767,5327,7846 +"YDR277C",903,894,934,257,1236,606,846,812,1309 +"YDR279W",436,506,460,383,546,310,335,402,572 +"YDR280W",448,501,640,1003,1121,300,395,419,613 +"YDR281C",34,48,68,80,79,12,11,31,54 +"YDR282C",459,457,375,284,346,505,327,332,587 +"YDR283C",1301,1291,897,624,888,820,825,788,1261 +"YDR284C",793,729,578,203,287,686,697,733,1127 +"YDR285W",385,302,194,162,198,353,269,299,470 +"YDR286C",193,197,126,77,147,362,195,232,323 +"YDR287W",625,637,460,342,313,702,615,583,1003 +"YDR288W",353,368,285,363,534,382,363,344,515 +"YDR289C",678,706,568,535,782,526,653,630,997 +"YDR291W",735,814,706,785,747,396,447,481,829 +"YDR292C",1205,1361,1268,1675,1986,994,1044,997,1465 +"YDR293C",5005,4214,2675,1095,1361,4651,4098,4216,6634 +"YDR294C",2436,2386,1838,1005,676,2624,2541,2102,3285 +"YDR295C",559,590,558,615,882,319,398,444,619 +"YDR296W",363,403,479,381,494,1949,589,407,622 +"YDR297W",791,1014,1589,2404,1906,477,504,610,995 +"YDR298C",2740,2840,2510,2453,2903,4461,3556,3012,3815 +"YDR299W",660,1090,1968,4186,2850,53,265,257,522 +"YDR300C",479,644,741,1140,1974,278,525,463,708 +"YDR301W",440,535,623,528,459,248,342,308,468 +"YDR302W",306,356,455,485,439,368,351,312,470 +"YDR303C",636,775,596,601,755,518,523,430,752 +"YDR304C",1334,1315,1198,1116,1253,2413,1429,1387,2279 +"YDR305C",446,456,312,211,293,581,450,461,683 +"YDR306C",1070,1018,662,276,392,1038,1021,1030,1458 +"YDR307W",1297,1208,873,468,532,877,820,883,1475 +"YDR308C",341,379,403,487,415,323,322,301,450 +"YDR309C",75,163,240,676,2089,106,54,64,59 +"YDR310C",1539,1577,1544,1661,1681,818,1185,1236,1914 +"YDR311W",708,682,679,569,590,307,508,596,834 +"YDR312W",526,584,719,978,1074,227,349,352,566 +"YDR313C",1690,1425,1034,502,457,1194,990,1147,2080 +"YDR314C",336,370,289,220,150,298,214,225,350 +"YDR315C",251,234,199,100,78,200,234,218,339 +"YDR316W",374,423,423,367,443,1738,481,380,527 +"YDR317W",234,267,199,225,243,204,242,215,333 +"YDR318W",431,434,351,220,247,419,416,347,530 +"YDR319C",647,567,423,302,273,486,536,585,1014 +"YDR320C",537,613,495,429,278,340,309,334,521 +"YDR320C-A",325,314,277,259,144,453,403,366,559 +"YDR321W",561,738,923,1656,2100,148,319,412,648 +"YDR322W",345,392,377,409,557,1381,421,336,469 +"YDR322C-A",1077,1110,945,733,1371,2073,1771,1323,1850 +"YDR323C",365,402,322,216,213,211,269,279,487 +"YDR324C",886,1445,2163,4968,3619,149,494,459,815 +"YDR325W",675,761,866,1059,1015,579,673,521,717 +"YDR326C",793,838,947,1466,938,544,560,526,828 +"YDR328C",2760,2480,2016,1341,1757,3606,3279,3253,4966 +"YDR329C",2334,2155,1466,451,829,2215,2101,2216,3599 +"YDR330W",1261,1130,793,158,205,1208,1010,1086,1828 +"YDR331W",400,470,542,613,729,283,305,290,402 +"YDR332W",555,566,421,327,369,458,430,384,707 +"YDR333C",900,960,905,975,1387,511,640,618,969 +"YDR334W",1308,1258,1039,884,924,1292,1289,920,1394 +"YDR335W",2405,2376,1976,1227,1141,1622,1681,1645,2716 +"YDR336W",256,260,264,241,270,188,188,210,322 +"YDR337W",400,472,453,463,560,1799,558,432,687 +"YDR338C",638,636,436,326,450,481,468,575,763 +"YDR339C",410,548,711,1290,1642,196,363,380,558 +"YDR341C",2678,3178,3248,5273,7042,1185,1574,1907,3163 +"YDR342C",2012,2002,1925,1062,2982,6727,4769,2885,3118 +"YDR343C",2716,1591,895,280,1298,5826,4186,4340,5690 +"YDR344C",4,1,5,1,8,21,15,9,16 +"YDR345C",316,428,583,816,527,194,247,246,438 +"YDR346C",2636,3216,3348,4668,3776,1766,1879,1822,3058 +"YDR347W",428,507,508,590,555,1598,445,373,560 +"YDR348C",504,704,878,1411,1485,547,596,537,648 +"YDR349C",912,1000,978,1138,1328,544,572,603,1043 +"YDR350C",752,766,742,542,490,581,576,531,887 +"YDR351W",971,1126,981,1137,985,511,642,686,1037 +"YDR352W",498,601,596,585,640,316,404,449,722 +"YDR353W",1218,1552,1798,2634,3221,1449,1213,1571,1935 +"YDR354W",1043,1161,1214,863,864,559,1016,1007,1440 +"YDR356W",1145,1212,893,547,565,974,786,825,1218 +"YDR357C",1119,895,636,420,422,1272,1297,1129,1735 +"YDR358W",1393,1196,601,42,125,1344,1058,1150,1765 +"YDR359C",1203,880,582,471,599,995,1083,910,1190 +"YDR361C",526,713,960,1666,1822,118,259,294,638 +"YDR362C",610,720,592,534,719,625,538,570,913 +"YDR363W",477,529,482,525,324,283,338,321,601 +"YDR363W-A",1741,1525,1261,1004,950,1737,1773,1653,2566 +"YDR364C",488,550,516,731,669,220,275,330,586 +"YDR365C",4701,4352,3764,4281,4555,4755,4065,3094,5562 +"YDR365W-B",12,9,11,9,6,6,6,7,8 +"YDR366C",7,14,4,8,7,14,6,4,5 +"YDR367W",422,440,416,361,417,427,381,361,586 +"YDR368W",1515,1497,1197,682,284,1219,1090,1292,2069 +"YDR369C",613,666,557,278,222,344,423,441,710 +"YDR370C",468,541,481,410,597,294,384,381,577 +"YDR371W",445,489,381,218,251,383,378,359,564 +"YDR372C",1344,1423,1167,1285,1690,980,1110,1026,1672 +"YDR373W",1004,1056,854,701,736,776,859,943,1630 +"YDR374C",10,17,21,18,18,9,6,7,17 +"YDR374W-A",255,220,181,140,174,209,194,242,348 +"YDR375C",362,376,355,254,402,1662,509,397,539 +"YDR376W",404,509,498,420,482,544,370,366,539 +"YDR377W",2312,2350,1765,1242,1827,3446,3394,2997,3739 +"YDR378C",519,488,379,332,576,477,574,639,1020 +"YDR379W",985,1099,935,626,873,668,756,780,1245 +"YDR379C-A",564,435,272,114,58,665,631,650,1070 +"YDR380W",1454,1570,1312,451,119,1249,1696,1688,2136 +"YDR381W",3546,3083,2534,2757,4261,3758,3495,3293,4935 +"YDR381C-A",262,300,244,145,248,574,222,252,442 +"YDR382W",3179,3911,4243,7760,12972,829,2131,2418,4708 +"YDR383C",283,263,265,149,120,212,215,216,414 +"YDR384C",8020,6257,3372,817,672,10711,10359,8753,13233 +"YDR385W",2012,2384,2371,3696,4701,421,532,853,2059 +"YDR386W",433,478,408,224,274,425,363,366,531 +"YDR387C",575,577,460,338,426,485,344,414,685 +"YDR388W",1746,1718,1306,855,616,1734,1581,1722,2828 +"YDR389W",703,700,589,508,804,814,798,534,819 +"YDR390C",1069,1054,861,786,1128,1011,1048,972,1503 +"YDR391C",291,287,205,244,226,369,250,295,493 +"YDR392W",618,676,549,404,594,493,520,557,861 +"YDR393W",315,401,384,295,414,636,349,305,503 +"YDR394W",3982,3650,2857,1836,1792,2976,3639,3460,5814 +"YDR395W",1037,1411,1888,4302,3798,307,563,538,889 +"YDR397C",700,658,647,920,914,610,709,916,1281 +"YDR398W",413,815,2020,4231,1745,65,181,189,384 +"YDR399W",2836,3724,4636,7232,10342,1386,2260,2629,3881 +"YDR400W",200,264,266,311,454,142,120,136,238 +"YDR402C",166,127,64,39,81,255,167,149,238 +"YDR403W",125,139,110,90,96,282,166,127,195 +"YDR404C",375,370,411,460,726,400,423,385,569 +"YDR405W",590,668,519,312,529,1942,909,689,985 +"YDR406W",890,913,640,322,356,889,613,650,1014 +"YDR407C",632,673,671,500,521,420,475,434,612 +"YDR408C",438,468,475,841,1308,488,419,439,691 +"YDR409W",635,755,533,460,581,533,538,522,737 +"YDR410C",241,270,212,257,450,161,199,216,356 +"YDR411C",711,614,460,200,355,745,742,745,1062 +"YDR412W",400,577,858,1826,2238,145,251,282,491 +"YDR414C",268,304,281,270,333,222,211,208,361 +"YDR415C",414,502,463,439,492,336,389,357,542 +"YDR416W",609,664,651,723,706,292,419,423,690 +"YDR418W",3418,3896,4104,7315,10606,1130,2661,2748,4876 +"YDR419W",562,672,619,536,625,378,402,404,709 +"YDR420W",1010,1035,965,1070,842,396,513,554,953 +"YDR421W",776,832,626,464,513,584,585,564,917 +"YDR422C",983,876,685,586,753,698,745,756,1204 +"YDR423C",548,612,423,244,383,449,489,498,775 +"YDR424C",482,429,317,222,258,624,527,575,887 +"YDR425W",504,572,372,118,220,427,435,434,582 +"YDR427W",3152,3010,2261,1777,1935,2721,3046,2756,4046 +"YDR428C",348,421,406,519,545,305,303,327,526 +"YDR429C",1760,2004,2433,4141,5413,1208,1543,1384,2315 +"YDR430C",747,909,752,543,504,2601,824,644,877 +"YDR432W",2069,2966,3528,5030,3202,1049,931,1119,2137 +"YDR434W",1091,1159,941,822,932,799,812,825,1260 +"YDR435C",406,387,268,71,154,631,418,496,753 +"YDR436W",789,759,498,195,324,878,685,669,1121 +"YDR437W",82,93,66,77,94,49,50,75,127 +"YDR438W",364,350,272,243,433,399,308,312,447 +"YDR439W",289,298,295,291,338,164,212,214,333 +"YDR440W",312,357,436,302,339,190,252,268,430 +"YDR441C",708,743,881,1102,1175,334,514,521,795 +"YDR443C",766,839,672,308,326,591,585,521,825 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+"YPR195C",47,43,47,21,42,54,55,37,51 +"YPR196W",281,320,294,281,381,219,222,238,350 +"YPR198W",682,656,617,593,549,443,477,528,792 +"YPR199C",456,463,441,392,436,386,423,408,709 +"YPR200C",60,56,24,29,49,68,53,60,74 +"YPR201W",171,178,136,67,84,133,137,165,222 +"YPR202W",6,10,8,3,11,4,4,2,3 +"YPR204W",57,60,65,36,73,59,42,41,68 +"Q0020",39,24,27,19,34,52,74,43,83 +"Q0055",1,11,7,7,3,11,15,12,24 +"Q0050",3,6,2,2,7,4,17,7,12 +"Q0130",1,3,3,2,1,3,3,4,7 +"Q0158",156,148,92,98,149,195,313,188,425 diff --git a/test_data/YMC/samplesheet_RCvsOX.csv b/test_data/YMC/samplesheet_RCvsOX.csv new file mode 100644 index 00000000..9748bc2b --- /dev/null +++ b/test_data/YMC/samplesheet_RCvsOX.csv @@ -0,0 +1,10 @@ +"sample","fase" +"Time.1","RC" +"Time.2","RC" +"Time.3","OX" +"Time.4","OX" +"Time.5","OX" +"Time.13","RC" +"Time.14","RC" +"Time.15","RC" +"Time.16","RC" From 6f8d5b069424ea34ec8f24789122133ace21f19d Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 15:28:43 +0200 Subject: [PATCH 08/15] upload mygene module with nf-core module install --- modules.json | 20 +++ modules/nf-core/mygene/main.nf | 2 +- modules/nf-core/mygene/templates/mygene.py | 166 +++++++++++++-------- 3 files changed, 124 insertions(+), 64 deletions(-) diff --git a/modules.json b/modules.json index ff141997..d4e06ef3 100644 --- a/modules.json +++ b/modules.json @@ -60,6 +60,26 @@ "git_sha": "9326d73af3fbe2ee90d9ce0a737461a727c5118e", "installed_by": ["modules"] }, + "mygene": { + "branch": "master", + "git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9", + "installed_by": ["modules"] + }, + "propr/grea": { + "branch": "master", + "git_sha": "71b1180a5a3de6398eb0eb4d55424cbda36f52d8", + "installed_by": ["modules"] + }, + "propr/propd": { + "branch": "master", + "git_sha": "08b360512467e8e7079f995bb7c981a7c204d00f", + "installed_by": ["modules"] + }, + "propr/propr": { + "branch": "master", + "git_sha": "c8b064f86eaa6c7ca89286bc12c0e517be0e6215", + "installed_by": ["modules"] + }, "proteus/readproteingroups": { "branch": "master", "git_sha": "a069b29783583c219c1f23ed3dcf64a5aee1340b", diff --git a/modules/nf-core/mygene/main.nf b/modules/nf-core/mygene/main.nf index 27066b71..25a21d8f 100644 --- a/modules/nf-core/mygene/main.nf +++ b/modules/nf-core/mygene/main.nf @@ -5,7 +5,7 @@ process MYGENE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mygene:3.2.2--pyh5e36f6f_0': - 'quay.io/biocontainers/mygene:3.2.2--pyh5e36f6f_0' }" + 'biocontainers/mygene:3.2.2--pyh5e36f6f_0' }" input: tuple val(meta), path(gene_list) diff --git a/modules/nf-core/mygene/templates/mygene.py b/modules/nf-core/mygene/templates/mygene.py index 201977a0..2717c467 100644 --- a/modules/nf-core/mygene/templates/mygene.py +++ b/modules/nf-core/mygene/templates/mygene.py @@ -23,13 +23,10 @@ class Arguments: """ Parses the argments, including the ones coming from $task.ext.args. """ + def __init__(self) -> None: self.input = "$gene_list" - self.prefix = ( - "$task.ext.prefix" - if "$task.ext.prefix" != "null" - else "$meta.id" - ) + self.prefix = "$task.ext.prefix" if "$task.ext.prefix" != "null" else "$meta.id" self.output_gmt = self.prefix + ".gmt" self.output_tsv = self.prefix + ".tsv" self.parse_ext_args("$task.ext.args") @@ -46,17 +43,49 @@ def parse_ext_args(self, args_string: str) -> None: args_list = shlex.split(args_string) # Split the string into a list of arguments parser = argparse.ArgumentParser() # input parameters - parser.add_argument('--columname', default='"gene_id"', help='Name of the column where the gene ids are stored in the input file. Default: gene_id') + parser.add_argument( + "--columname", + default="gene_id", + help="Name of the column where the gene ids are stored in the input file. Default: gene_id", + ) # filtering parameters - parser.add_argument('--species', default=None, help="Comma separated of common name of the species or taxon ids") - parser.add_argument('--go_category', default=None, help="Comma separated list of GO categories to keep. Default: all") - parser.add_argument('--go_evidence', default=None, help="Comma separated list of GO evidence codes to keep. Default: all") + parser.add_argument( + "--species", + default=None, + help="Comma separated of common name of the species or taxon ids", + ) + parser.add_argument( + "--go_category", + default=None, + help="Comma separated list of GO categories to keep. Default: all", + ) + parser.add_argument( + "--go_evidence", + default=None, + help="Comma separated list of GO evidence codes to keep. Default: all", + ) # additional parameters for querymany - parser.add_argument('--scopes', default=None, help="Comma separated list of scopes to search for.") - parser.add_argument('--entrezonly', default=False, help="When true, the query returns only the hits with valid Entrez gene ids. Default: false.") - parser.add_argument('--ensemblonly', default=False, help="When true, the query returns only the hits with valid Ensembl gene ids. Default: False") + parser.add_argument( + "--scopes", + default=None, + help="Comma separated list of scopes to search for.", + ) + parser.add_argument( + "--entrezonly", + default=False, + help="When true, the query returns only the hits with valid Entrez gene ids. Default: false.", + ) + parser.add_argument( + "--ensemblonly", + default=False, + help="When true, the query returns only the hits with valid Ensembl gene ids. Default: False", + ) # output parameters - parser.add_argument('--generate_tsv', default=False, help="Also generate a tsv file with the gene based information. Default: False") + parser.add_argument( + "--generate_tsv", + default=False, + help="Also generate a tsv file with the gene based information. Default: False", + ) args = parser.parse_args(args_list) # Convert "null" values to default values @@ -135,7 +164,17 @@ class MyGene: of the query gene. Then, it queries for the annotations, and parses the go terms all together with all the other information. """ - def __init__(self, query: list, species: str, scopes: str, entrezonly: bool, ensemblonly: bool, go_category: str = None, go_evidence: str = None) -> None: + + def __init__( + self, + query: list, + species: str, + scopes: str, + entrezonly: bool, + ensemblonly: bool, + go_category: str = None, + go_evidence: str = None, + ) -> None: self.query = query self.fields = "go,symbol,name,taxid" self.species = species @@ -158,9 +197,9 @@ def query2idmap(self) -> dict: species=self.species, entrezonly=self.entrezonly, ensemblonly=self.ensemblonly, - returnall=True + returnall=True, ) - return {dic['_id']: dic['query'] for dic in q['out'] if '_id' in dic} + return {dic["_id"]: dic["query"] for dic in q["out"] if "_id" in dic} def id2info(self) -> list: """ @@ -177,22 +216,23 @@ def parse_go_based_info(self) -> dict: """ info = {} for dic in self.id2info(): - - if 'go' not in dic: + if "go" not in dic: continue if self.go_category: - dic['go'] = {category: dic['go'][category] for category in self.go_category.split(",") if category in dic['go']} - for category, go_list in dic['go'].items(): + dic["go"] = { + category: dic["go"][category] for category in self.go_category.split(",") if category in dic["go"] + } + for category, go_list in dic["go"].items(): if not isinstance(go_list, list): go_list = [go_list] for go in go_list: - if (self.go_evidence) and (go['evidence'] not in self.go_evidence.split(",")): + if (self.go_evidence) and (go["evidence"] not in self.go_evidence.split(",")): continue - if go['id'] not in info: - info[go['id']] = [go['term'], self.idmap[dic['_id']]] + if go["id"] not in info: + info[go["id"]] = [go["term"], self.idmap[dic["_id"]]] else: - info[go['id']].append(self.idmap[dic['_id']]) + info[go["id"]].append(self.idmap[dic["_id"]]) return info def parse_gene_based_info(self) -> dict: @@ -206,30 +246,31 @@ def parse_gene_based_info(self) -> dict: """ info = {} for dic in self.id2info(): - - if 'go' not in dic: + if "go" not in dic: continue if self.go_category: - dic['go'] = {category: dic['go'][category] for category in self.go_category.split(",") if category in dic['go']} - for category, go_list in dic['go'].items(): + dic["go"] = { + category: dic["go"][category] for category in self.go_category.split(",") if category in dic["go"] + } + for category, go_list in dic["go"].items(): if not isinstance(go_list, list): go_list = [go_list] for go in go_list: - if (self.go_evidence) and (go['evidence'] not in self.go_evidence.split(",")): + if (self.go_evidence) and (go["evidence"] not in self.go_evidence.split(",")): continue current_info = { - 'query': self.idmap[dic['_id']], - 'mygene_id': dic['_id'], - 'go_id': go['id'], - 'go_term': go['term'], - 'go_evidence': go['evidence'], - 'go_category': category, - 'symbol': dic['symbol'], - 'name': dic['name'], - 'taxid': dic['taxid'] + "query": self.idmap[dic["_id"]], + "mygene_id": dic["_id"], + "go_id": go["id"], + "go_term": go["term"], + "go_evidence": go["evidence"], + "go_category": category, + "symbol": dic["symbol"], + "name": dic["name"], + "taxid": dic["taxid"], } - info[self.idmap[dic['_id']]] = current_info + info[self.idmap[dic["_id"]]] = current_info return info def parse_and_save_to_gmt(self, filename: str) -> list: @@ -239,7 +280,7 @@ def parse_and_save_to_gmt(self, filename: str) -> list: """ info = self.parse_go_based_info() info = dict(sorted(info.items(), key=lambda x: x[0])) - with open(filename, 'w') as f: + with open(filename, "w") as f: for go_id, go_list in info.items(): tmp = sorted(go_list[1:]) f.write(go_id + "\\t" + go_list[0] + "\\t" + "\\t".join(tmp) + "\\n") @@ -251,7 +292,7 @@ def parse_and_save_to_tsv(self, filename: str) -> None: The final tsv output will be sorted following the input query gene list order. """ info = self.parse_gene_based_info() - with open(filename, 'w') as f: + with open(filename, "w") as f: f.write("\\t".join(info[self.query[0]].keys()) + "\\n") for gene in self.query: # sorted by query gene list if gene in info: @@ -260,23 +301,22 @@ def parse_and_save_to_tsv(self, filename: str) -> None: def load_list(filename: str, columname: str) -> list: - """ - It loads the list of gene ids from a file. - The columname is the name of the column where the gene ids are stored. - """ - if filename.split('.')[-1] == 'tsv': - sep = "\\t" - elif filename.split('.')[-1] == 'csv': - sep = "," - else: - raise ValueError("The input file extension should be either tsv or csv.") - with open(filename, 'r') as f: - idx = f.readline().strip().split(sep).index(columname) - return [line.strip().split(sep)[idx] for line in f] + """ + It loads the list of gene ids from a file. + The columname is the name of the column where the gene ids are stored. + """ + if filename.split(".")[-1] == "tsv": + sep = "\\t" + elif filename.split(".")[-1] == "csv": + sep = "," + else: + raise ValueError("The input file extension should be either tsv or csv.") + with open(filename, "r") as f: + idx = f.readline().strip().split(sep).index(columname) + return [line.strip().split(sep)[idx] for line in f] if __name__ == "__main__": - # parse and print arguments args = Arguments() args.print_args() @@ -286,14 +326,14 @@ def load_list(filename: str, columname: str) -> list: # run mygene api mg = MyGene( - gene_list, - species=args.species, - scopes=args.scopes, - entrezonly=args.entrezonly, - ensemblonly=args.ensemblonly, - go_category=args.go_category, - go_evidence=args.go_evidence - ) + gene_list, + species=args.species, + scopes=args.scopes, + entrezonly=args.entrezonly, + ensemblonly=args.ensemblonly, + go_category=args.go_category, + go_evidence=args.go_evidence, + ) # parse annotations and save output files mg.parse_and_save_to_gmt(args.output_gmt) From 969d15ae3a189fe271d67db887674e8a2003ed89 Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 15:45:39 +0200 Subject: [PATCH 09/15] fix linting errors --- assets/tools_samplesheet.csv | 2 +- conf/crg.config | 30 +- conf/modules_coda.config | 2 +- main_coda.nf | 6 +- modules/local/filtervar/main.nf | 2 +- modules/local/filtervar/templates/filtervar.R | 8 +- nextflow_coda.config | 4 +- subworkflows/local/correlation/main.nf | 4 +- subworkflows/local/differential/main.nf | 4 +- subworkflows/local/enrichment/main.nf | 6 +- subworkflows/local/experimental/main.nf | 10 +- subworkflows/local/variable_selection/main.nf | 6 +- test_data/YMC/counts_sin0.csv | 5840 ----------------- test_data/YMC/samplesheet_RCvsOX.csv | 10 - 14 files changed, 42 insertions(+), 5892 deletions(-) delete mode 100644 test_data/YMC/counts_sin0.csv delete mode 100644 test_data/YMC/samplesheet_RCvsOX.csv diff --git a/assets/tools_samplesheet.csv b/assets/tools_samplesheet.csv index f6147f34..1c16d64b 100644 --- a/assets/tools_samplesheet.csv +++ b/assets/tools_samplesheet.csv @@ -3,4 +3,4 @@ diff_prop,propd, --adjacency true --permutation 100 --fixseed true, , ,,, , ,, filtered_pcor,propd, --adjacency true --permutation 100 --fixseed true, , ,propr, --permutation 10 --adjacency true --cutoff_min 0.005 --cutoff_max 0.5 --cutoff_interval 0.01 --metric pcor.bshrink, , , filtervar, prop,, , , ,propr, --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --fixseed true --metric rho --permutation 100 --adjacency true, , , , diff_grea,propd,--group_col fase --adjacency true --permutation 10,grea, --permutation 10, , , , ,, -deseq2,deseq2,,gsea,,,,,,, \ No newline at end of file +deseq2,deseq2,,gsea,,,,,,, diff --git a/conf/crg.config b/conf/crg.config index 07da3727..29d4366e 100644 --- a/conf/crg.config +++ b/conf/crg.config @@ -1,10 +1,10 @@ params { - config_profile_name = 'CRG profile' - config_profile_description = 'Configuration to run on CRG cluster' + config_profile_name = 'CRG profile' + config_profile_description = 'Configuration to run on CRG cluster' - max_cpus = 64 - max_memory = 100.GB - max_time = 48.h + max_cpus = 64 + max_memory = 100.GB + max_time = 48.h } @@ -14,18 +14,18 @@ process { //errorStrategy = params.err_start withLabel:process_low { - queue = 'cn-el7,short-centos79' - cpus = { check_max( 2 , 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + queue = 'cn-el7,short-centos79' + cpus = { check_max( 2 , 'cpus' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_medium{ - queue = 'cn-el7,short-centos79' - cpus = { check_max( 6 , 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + queue = 'cn-el7,short-centos79' + cpus = { check_max( 6 , 'cpus' ) } + memory = { check_max( 36.GB * task.attempt, 'memory' ) } + time = { check_max( 8.h * task.attempt, 'time' ) } } - withLabel:process_high { + withLabel:process_high { queue = 'cn-el7,long-centos79' cpus = { check_max( 12 , 'cpus' ) } memory = { check_max( 56.GB * task.attempt, 'memory' ) } @@ -38,4 +38,4 @@ process { singularity { enabled = true cacheDir = 'singularity_cache' -} \ No newline at end of file +} diff --git a/conf/modules_coda.config b/conf/modules_coda.config index a783c00e..44d272e4 100644 --- a/conf/modules_coda.config +++ b/conf/modules_coda.config @@ -42,4 +42,4 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } -} \ No newline at end of file +} diff --git a/main_coda.nf b/main_coda.nf index 6a62390e..ca9043bc 100644 --- a/main_coda.nf +++ b/main_coda.nf @@ -1,7 +1,7 @@ // include { PROPR_PROPR } from '../../../modules/nf-core/propr/propr/main' // include { PROPR_PROPD } from '../../../modules/nf-core/propr/propd/main' // include { PROPR_GREA } from '../../../modules/nf-core/propr/grea/main' -// include { MYGENE } from '../../../modules/nf-core/mygene/main' +// include { MYGENE } from '../../../modules/nf-core/mygene/main' include { EXPERIMENTAL } from './subworkflows/experimental/main.nf' include { fromSamplesheet } from 'plugin/nf-validation' @@ -11,11 +11,11 @@ include { fromSamplesheet } from 'plugin/nf-validation' Counts_ch = Channel.fromPath("../YMC/counts_sin0.csv") Sample_ch = Channel.fromPath("../YMC/samplesheet_RCvsOX.csv") - .map{ it -> [[id: 'YMC'], it]} + .map{ it -> [[id: 'YMC'], it]} ch_samples_and_matrix = Sample_ch.combine(Counts_ch) -// Convert the samplesheet.csv in a channel with the proper format +// Convert the samplesheet.csv in a channel with the proper format ch_tools = Channel.fromSamplesheet('tools') diff --git a/modules/local/filtervar/main.nf b/modules/local/filtervar/main.nf index bf8e3ae2..5d9c39c8 100644 --- a/modules/local/filtervar/main.nf +++ b/modules/local/filtervar/main.nf @@ -20,4 +20,4 @@ process FILTERVAR { script: template 'filtervar.R' -} \ No newline at end of file +} diff --git a/modules/local/filtervar/templates/filtervar.R b/modules/local/filtervar/templates/filtervar.R index cf5159c9..7b662626 100644 --- a/modules/local/filtervar/templates/filtervar.R +++ b/modules/local/filtervar/templates/filtervar.R @@ -189,23 +189,23 @@ A\$per_gene <- per_gene_connection A <- A[order(A\$per_gene, decreasing = TRUE),] -# Define selection criteria +# Define selection criteria max_gene_number <- ncol(count)*10 # 10x samples for technical reasons (pcor) -#Calculate connection threshold +#Calculate connection threshold total_connections <- sum(per_gene_connection)/2 # 2 because the matrix is symmetric possible_connections <- nrow(count)*(nrow(count)-1)/2 percentage_expected <- total_connections/possible_connections connection_threshold <- percentage_expected * nrow(count) -# Filter count matrix according to selected genes +# Filter count matrix according to selected genes col_genes <- which(names(count) == opt\$features_id_col) if (opt\$filterVar == 'yes'){ - # select only differentially proportional genes + # select only differentially proportional genes top_genes <- rownames(A[which(A\$per_gene > connection_threshold),]) count_filtered <- count[count[,col_genes] %in% top_genes,] warning("non differentially proportional genes were removed before correlation analysis") diff --git a/nextflow_coda.config b/nextflow_coda.config index 3ed7f425..23d475f4 100644 --- a/nextflow_coda.config +++ b/nextflow_coda.config @@ -6,7 +6,7 @@ params.validationSkipDuplicateCheck = true params.publish_dir_mode = 'copy' params.pathway = 'all' //params.maxRetries = 0 -includeConfig 'conf/modules.config' // now it should refer to modules_coda.config +includeConfig 'conf/modules.config' // now it should refer to modules_coda.config @@ -52,4 +52,4 @@ def check_max(obj, type) { return obj } } -} \ No newline at end of file +} diff --git a/subworkflows/local/correlation/main.nf b/subworkflows/local/correlation/main.nf index 5aaad2e2..5bcaa808 100644 --- a/subworkflows/local/correlation/main.nf +++ b/subworkflows/local/correlation/main.nf @@ -22,7 +22,7 @@ workflow CORRELATION { .set { ch_counts_cor } // Hacer un branch del channel para coger las counts normales cuando no hay variable selection - + ch_counts_cor.propr .branch{ no_sel: it[0]["sel_method"] == null @@ -45,4 +45,4 @@ workflow CORRELATION { matrix = ch_matrix adjacency = ch_adjacency -} \ No newline at end of file +} diff --git a/subworkflows/local/differential/main.nf b/subworkflows/local/differential/main.nf index 15948b9c..ccea968a 100644 --- a/subworkflows/local/differential/main.nf +++ b/subworkflows/local/differential/main.nf @@ -21,7 +21,7 @@ workflow DIFFERENTIAL { deseq2: it[0]["diff_method"] == "deseq2" } .set { ch_counts_tools } - + PROPD(ch_counts_tools.propd, ch_samplesheet) ch_results = PROPD.out.results ch_adjacency = PROPD.out.adj @@ -30,4 +30,4 @@ workflow DIFFERENTIAL { results = ch_results adjacency = ch_adjacency -} \ No newline at end of file +} diff --git a/subworkflows/local/enrichment/main.nf b/subworkflows/local/enrichment/main.nf index 442014a3..b19f96fc 100644 --- a/subworkflows/local/enrichment/main.nf +++ b/subworkflows/local/enrichment/main.nf @@ -8,8 +8,8 @@ include { MYGENE } from "../../modules/nf-core/mygene/main.nf" workflow ENRICHMENT { take: ch_diff_adjacency - ch_cor_adjacency - ch_counts + ch_cor_adjacency + ch_counts main: @@ -43,4 +43,4 @@ workflow ENRICHMENT { emit: enriched_diff = ch_enriched_diff enriched_cor = ch_enriched_cor -} \ No newline at end of file +} diff --git a/subworkflows/local/experimental/main.nf b/subworkflows/local/experimental/main.nf index 6e26eb6d..62d51241 100644 --- a/subworkflows/local/experimental/main.nf +++ b/subworkflows/local/experimental/main.nf @@ -37,7 +37,7 @@ workflow EXPERIMENTAL { } .set { ch_counts_tools } - // Perform CODA analysis + // Perform CODA analysis ch_out = Channel.empty() // Perform differential analysis @@ -48,10 +48,10 @@ workflow EXPERIMENTAL { // Perform variable selection ch_counts_filtered = VARIABLE_SELECTION(ch_diff_adjacency, ch_counts) - + //VARIABLE_SELECTION.out.count.view() - // Perform correlation analysis + // Perform correlation analysis CORRELATION(ch_counts, ch_tools, ch_counts_filtered) ch_matrix = CORRELATION.out.matrix ch_cor_adjacency = CORRELATION.out.adjacency @@ -59,14 +59,14 @@ workflow EXPERIMENTAL { //ch_diff_adjacency.view() //ch_cor_adjacency.view() - + // Perform enrichment analysis ENRICHMENT(ch_diff_adjacency, ch_cor_adjacency, ch_counts) ch_enriched_cor = ENRICHMENT.out.enriched_cor ch_enriched_diff = ENRICHMENT.out.enriched_diff ch_out.mix(ch_enriched_diff, ch_enriched_cor) - + emit: output = ch_out diff --git a/subworkflows/local/variable_selection/main.nf b/subworkflows/local/variable_selection/main.nf index d7a176c8..f914473c 100644 --- a/subworkflows/local/variable_selection/main.nf +++ b/subworkflows/local/variable_selection/main.nf @@ -16,7 +16,7 @@ workflow VARIABLE_SELECTION { .combine(ch_adj) //.view() .map{ - counts, meta, adj -> + counts, meta, adj -> [ meta, counts, adj] } //.view() @@ -34,7 +34,7 @@ workflow VARIABLE_SELECTION { ch_counts_cor = FILTERVAR.out.count //ch_counts_cor.view() - + emit: count = ch_counts_cor -} \ No newline at end of file +} diff --git a/test_data/YMC/counts_sin0.csv b/test_data/YMC/counts_sin0.csv deleted file mode 100644 index 58ea62af..00000000 --- a/test_data/YMC/counts_sin0.csv +++ /dev/null @@ -1,5840 +0,0 @@ -"gene_id","Time.1","Time.2","Time.3","Time.4","Time.5","Time.13","Time.14","Time.15","Time.16" -"YAL068C",57,52,82,93,66,12,33,34,52 -"YAL063C",82,94,62,69,99,99,64,72,105 -"YAL062W",2280,2753,2819,2270,1033,2942,1535,2444,4300 -"YAL061W",2970,2391,1049,64,170,4379,2215,2849,4953 -"YAL060W",2354,1727,1039,378,578,5618,2218,2790,4385 -"YAL059W",339,534,832,1966,2627,51,185,189,360 -"YAL058W",362,459,447,574,546,229,266,279,491 -"YAL056W",1440,1269,894,233,393,1094,1083,1122,1763 -"YAL055W",266,305,255,61,108,190,246,277,477 -"YAL054C",27781,19019,8956,842,151,65763,49692,34469,45068 -"YAL053W",2027,2120,2779,3995,1796,963,1298,1864,2887 -"YAL051W",738,774,529,417,516,471,515,590,849 -"YAL049C",1752,1677,1138,592,382,1650,1602,1692,2793 -"YAL048C",594,557,428,361,305,434,393,401,619 -"YAL047C",361,393,343,276,335,195,225,222,341 -"YAL046C",212,223,211,170,207,377,201,221,344 -"YAL044W-A",543,477,401,403,350,566,570,599,895 -"YAL044C",1313,1345,1376,1512,1792,1237,1033,1109,1959 -"YAL043C",662,765,740,610,608,421,524,478,781 -"YAL042W",1402,1561,1514,1458,1497,1612,1611,1525,2301 -"YAL041W",874,1009,931,806,780,569,603,541,939 -"YAL040C",461,496,781,1188,1398,268,354,485,527 -"YAL039C",597,784,1003,891,658,1037,770,694,1154 -"YAL038W",58112,51535,41160,35725,15242,7632,8910,23994,59573 -"YAL037C-A",17,15,10,6,9,3,2,7,16 -"YAL037W",136,135,103,97,123,92,104,132,188 -"YAL036C",585,819,1099,2182,1675,86,371,381,651 -"YAL035W",3563,4130,4675,7945,6950,2337,3169,2701,4412 -"YAL034W-A",189,173,127,128,290,218,182,147,226 -"YAL034C",1341,1171,699,345,283,945,912,906,1595 -"YAL033W",148,157,186,238,434,150,148,137,241 -"YAL032C",365,410,408,281,374,531,506,417,632 -"YAL031C",584,509,439,278,434,432,419,392,628 -"YAL030W",686,630,442,216,153,662,613,618,1098 -"YAL029C",784,1113,1433,2741,957,506,615,538,774 -"YAL028W",307,292,174,43,34,287,244,254,388 -"YAL027W",457,449,256,106,267,611,522,515,690 -"YAL026C",924,1013,1035,1041,887,589,659,586,1017 -"YNCA0001W",3,5,3,8,6,2,2,2,2 -"YAL025C",594,1044,2169,5174,3574,39,286,273,530 -"YAL024C",281,311,342,393,397,170,232,172,241 -"YAL023C",1330,1558,1528,2354,2915,1130,1206,1067,1590 -"YAL022C",586,667,687,756,872,518,617,581,812 -"YAL021C",1123,1192,1026,1191,1137,809,948,806,1318 -"YAL020C",224,220,254,256,256,205,192,225,394 -"YAL019W",610,799,1044,1726,1689,175,292,266,525 -"YAL018C",53,49,49,34,44,38,30,35,73 -"YAL017W",1716,1423,967,212,299,1823,1233,1198,2090 -"YAL016W",3105,2860,2027,1115,1273,2640,2398,2550,3939 -"YAL015C",384,440,423,525,425,672,341,326,520 -"YAL014C",485,486,486,408,373,399,451,448,714 -"YAL013W",522,532,514,478,603,469,544,503,828 -"YAL012W",1420,2450,4168,10720,7247,527,834,742,1259 -"YAL011W",438,392,392,367,451,299,391,328,528 -"YAL010C",512,491,465,303,178,305,373,351,540 -"YAL009W",434,416,380,297,336,288,348,332,619 -"YAL008W",1069,952,631,323,232,1182,834,908,1585 -"YAL007C",403,451,445,469,530,362,384,348,528 -"YAL005C",39259,28272,16583,3934,2053,32018,23096,25421,47879 -"YAL003W",6226,6713,6934,10417,11213,1064,2494,2881,6539 -"YNCA0003W",28,22,28,40,30,2,11,9,33 -"YAL002W",862,914,757,563,520,453,508,493,847 -"YAL001C",1160,1147,944,515,621,950,841,877,1373 -"YAR002W",553,606,721,1095,883,320,423,467,696 -"YAR002C-A",1296,1328,1228,1305,1661,1263,982,1027,1821 -"YAR003W",391,369,347,338,550,317,299,319,484 -"YAR007C",1489,1606,1312,665,1118,1083,1052,1353,1918 -"YAR008W",192,281,273,215,398,152,153,242,249 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-"YDL155W",600,616,652,695,735,657,604,553,860 -"YDL154W",378,348,268,168,309,398,309,283,468 -"YDL153C",1166,1494,2101,4702,4840,193,613,634,1268 -"YDL150W",435,572,761,1476,1506,141,342,315,577 -"YDL149W",844,844,605,144,178,520,535,552,996 -"YDL148C",699,1191,1890,4386,3770,59,356,281,628 -"YDL147W",6863,6186,4603,3548,3450,4964,5653,5187,7623 -"YDL146W",228,213,145,109,172,220,177,185,270 -"YDL145C",2407,2588,2389,2533,2709,2585,2206,1868,2764 -"YDL144C",948,1054,957,844,642,926,929,900,1474 -"YDL143W",2538,2763,2664,3326,3680,1725,2296,2255,3488 -"YDL142C",369,404,279,139,176,410,362,383,524 -"YDL141W",636,709,625,586,621,406,491,430,676 -"YDL140C",3724,3713,3576,3904,3677,2364,2700,2396,3601 -"YDL139C",121,104,93,60,51,62,44,60,147 -"YDL138W",730,949,1192,1306,796,552,679,624,910 -"YDL137W",4292,3960,3056,2190,1925,6521,5478,5420,7775 -"YDL136W",996,1190,1294,2088,3522,237,646,710,1272 -"YDL135C",914,972,811,530,566,1039,885,862,1208 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-"YDR196C",848,812,572,256,250,1135,968,953,1449 -"YDR197W",384,403,322,248,237,530,354,318,514 -"YDR198C",449,549,506,642,659,284,343,344,543 -"YDR200C",672,701,559,384,512,669,636,590,842 -"YDR201W",312,250,220,164,202,399,398,332,496 -"YDR202C",1043,975,628,249,241,990,840,961,1417 -"YDR204W",1327,1168,765,202,109,1376,1177,1202,1852 -"YDR205W",395,393,392,304,368,291,298,344,465 -"YDR206W",1444,1576,1439,1647,1652,736,919,948,1615 -"YDR207C",733,905,928,1051,832,556,581,579,918 -"YDR208W",1412,1547,1636,1513,1101,1356,1282,1047,1557 -"YDR209C",68,84,66,113,110,102,101,75,94 -"YDR210W-B",13,19,16,13,15,8,11,5,15 -"YDR210C-D",19,16,14,27,19,8,4,9,10 -"YDR211W",1262,1569,1819,2891,3047,541,814,940,1399 -"YDR212W",2872,3232,3259,4208,3398,1600,2274,2165,3646 -"YDR213W",327,431,487,527,517,97,177,212,295 -"YDR214W",6997,5908,4054,1393,871,4916,4684,5425,10337 -"YDR215C",12,13,11,1,6,10,9,10,16 -"YDR216W",2647,2528,1686,458,703,2215,1928,1897,2977 -"YDR217C",822,1003,969,1226,951,352,462,458,797 -"YDR218C",398,343,256,133,97,249,270,329,591 -"YDR219C",704,677,561,396,595,777,662,642,923 -"YDR221W",1089,1206,1061,833,505,630,618,620,1115 -"YDR222W",479,608,655,1360,458,323,286,338,589 -"YDR223W",2071,1674,945,181,151,3189,1625,1769,2950 -"YDR224C",6159,5872,4590,3429,3656,6651,4813,4605,7860 -"YDR225W",5459,4454,3026,2319,2216,6080,5630,6127,10355 -"YDR226W",2504,2659,2460,3640,4991,2439,2051,2474,4039 -"YDR227W",1246,1330,1099,1072,1003,658,853,798,1331 -"YDR228C",858,797,646,652,1180,761,695,723,1122 -"YDR229W",790,852,633,352,356,767,699,788,1231 -"YDR231C",987,1009,719,371,450,1310,1103,1127,1635 -"YDR232W",1797,2122,2631,4237,2517,905,1325,1281,2004 -"YDR233C",3717,3607,3322,3856,4589,1979,2843,2734,4141 -"YDR234W",1779,3256,4590,9017,9837,282,621,614,1262 -"YDR235W",408,437,409,451,587,300,348,301,435 -"YDR236C",397,387,322,248,259,299,314,362,624 -"YDR237W",362,397,402,414,550,1906,496,338,490 -"YDR238C",3134,3406,3145,3394,3035,2634,2465,2275,3435 -"YDR239C",469,509,456,432,461,285,306,307,549 -"YDR240C",308,375,349,375,436,174,203,219,369 -"YDR242W",612,718,538,433,437,330,377,378,695 -"YDR243C",313,404,427,457,266,183,193,188,323 -"YDR244W",1233,1431,936,469,699,2307,1522,1281,1586 -"YDR245W",932,1195,1413,2031,2125,693,865,819,1199 -"YDR246W",548,545,386,166,189,389,448,428,772 -"YDR246W-A",23,14,10,5,9,37,25,22,49 -"YDR247W",724,568,300,85,254,787,706,666,987 -"YDR248C",1110,1382,1235,1071,493,841,738,852,1603 -"YDR249C",149,195,212,277,319,98,91,114,171 -"YDR251W",1078,1084,806,535,855,1182,906,906,1300 -"YDR252W",85,72,78,56,31,84,107,84,134 -"YDR253C",597,746,843,1312,526,255,453,471,775 -"YDR254W",608,502,320,172,283,530,502,453,736 -"YDR255C",855,769,486,154,281,585,567,603,904 -"YDR256C",10753,8212,4002,404,354,43475,29705,19465,22136 -"YDR257C",362,497,541,852,1011,243,320,315,413 -"YDR258C",11660,8819,5236,1133,1254,14785,7934,8183,14886 -"YDR259C",186,236,351,411,306,207,268,187,233 -"YDR260C",350,336,300,343,295,224,277,325,510 -"YDR261C",163,206,198,264,328,304,171,151,237 -"YDR261W-B",43,61,61,19,15,28,18,9,36 -"YDR261C-D",50,55,56,32,54,37,40,39,65 -"YNCD0020W",56,37,23,18,5,27,28,35,55 -"YDR262W",3255,2858,1987,1176,1054,1822,1955,2278,4505 -"YDR263C",114,115,72,54,144,201,131,97,176 -"YDR264C",1497,1675,1562,1190,1215,1105,1203,1288,1835 -"YDR265W",431,470,361,219,283,423,397,392,609 -"YDR266C",465,562,751,1256,1248,255,392,352,512 -"YDR267C",453,515,548,679,717,351,408,403,610 -"YDR268W",133,159,170,170,195,532,159,129,155 -"YDR270W",735,747,646,227,242,762,564,517,847 -"YDR272W",1842,1784,1415,1048,1146,1651,1605,1734,2634 -"YDR273W",158,132,104,97,151,222,140,139,257 -"YDR274C",180,159,114,68,85,200,211,156,236 -"YDR275W",1696,1807,1219,437,630,803,607,815,1964 -"YDR276C",4621,3514,2313,1149,1296,6672,5767,5327,7846 -"YDR277C",903,894,934,257,1236,606,846,812,1309 -"YDR279W",436,506,460,383,546,310,335,402,572 -"YDR280W",448,501,640,1003,1121,300,395,419,613 -"YDR281C",34,48,68,80,79,12,11,31,54 -"YDR282C",459,457,375,284,346,505,327,332,587 -"YDR283C",1301,1291,897,624,888,820,825,788,1261 -"YDR284C",793,729,578,203,287,686,697,733,1127 -"YDR285W",385,302,194,162,198,353,269,299,470 -"YDR286C",193,197,126,77,147,362,195,232,323 -"YDR287W",625,637,460,342,313,702,615,583,1003 -"YDR288W",353,368,285,363,534,382,363,344,515 -"YDR289C",678,706,568,535,782,526,653,630,997 -"YDR291W",735,814,706,785,747,396,447,481,829 -"YDR292C",1205,1361,1268,1675,1986,994,1044,997,1465 -"YDR293C",5005,4214,2675,1095,1361,4651,4098,4216,6634 -"YDR294C",2436,2386,1838,1005,676,2624,2541,2102,3285 -"YDR295C",559,590,558,615,882,319,398,444,619 -"YDR296W",363,403,479,381,494,1949,589,407,622 -"YDR297W",791,1014,1589,2404,1906,477,504,610,995 -"YDR298C",2740,2840,2510,2453,2903,4461,3556,3012,3815 -"YDR299W",660,1090,1968,4186,2850,53,265,257,522 -"YDR300C",479,644,741,1140,1974,278,525,463,708 -"YDR301W",440,535,623,528,459,248,342,308,468 -"YDR302W",306,356,455,485,439,368,351,312,470 -"YDR303C",636,775,596,601,755,518,523,430,752 -"YDR304C",1334,1315,1198,1116,1253,2413,1429,1387,2279 -"YDR305C",446,456,312,211,293,581,450,461,683 -"YDR306C",1070,1018,662,276,392,1038,1021,1030,1458 -"YDR307W",1297,1208,873,468,532,877,820,883,1475 -"YDR308C",341,379,403,487,415,323,322,301,450 -"YDR309C",75,163,240,676,2089,106,54,64,59 -"YDR310C",1539,1577,1544,1661,1681,818,1185,1236,1914 -"YDR311W",708,682,679,569,590,307,508,596,834 -"YDR312W",526,584,719,978,1074,227,349,352,566 -"YDR313C",1690,1425,1034,502,457,1194,990,1147,2080 -"YDR314C",336,370,289,220,150,298,214,225,350 -"YDR315C",251,234,199,100,78,200,234,218,339 -"YDR316W",374,423,423,367,443,1738,481,380,527 -"YDR317W",234,267,199,225,243,204,242,215,333 -"YDR318W",431,434,351,220,247,419,416,347,530 -"YDR319C",647,567,423,302,273,486,536,585,1014 -"YDR320C",537,613,495,429,278,340,309,334,521 -"YDR320C-A",325,314,277,259,144,453,403,366,559 -"YDR321W",561,738,923,1656,2100,148,319,412,648 -"YDR322W",345,392,377,409,557,1381,421,336,469 -"YDR322C-A",1077,1110,945,733,1371,2073,1771,1323,1850 -"YDR323C",365,402,322,216,213,211,269,279,487 -"YDR324C",886,1445,2163,4968,3619,149,494,459,815 -"YDR325W",675,761,866,1059,1015,579,673,521,717 -"YDR326C",793,838,947,1466,938,544,560,526,828 -"YDR328C",2760,2480,2016,1341,1757,3606,3279,3253,4966 -"YDR329C",2334,2155,1466,451,829,2215,2101,2216,3599 -"YDR330W",1261,1130,793,158,205,1208,1010,1086,1828 -"YDR331W",400,470,542,613,729,283,305,290,402 -"YDR332W",555,566,421,327,369,458,430,384,707 -"YDR333C",900,960,905,975,1387,511,640,618,969 -"YDR334W",1308,1258,1039,884,924,1292,1289,920,1394 -"YDR335W",2405,2376,1976,1227,1141,1622,1681,1645,2716 -"YDR336W",256,260,264,241,270,188,188,210,322 -"YDR337W",400,472,453,463,560,1799,558,432,687 -"YDR338C",638,636,436,326,450,481,468,575,763 -"YDR339C",410,548,711,1290,1642,196,363,380,558 -"YDR341C",2678,3178,3248,5273,7042,1185,1574,1907,3163 -"YDR342C",2012,2002,1925,1062,2982,6727,4769,2885,3118 -"YDR343C",2716,1591,895,280,1298,5826,4186,4340,5690 -"YDR344C",4,1,5,1,8,21,15,9,16 -"YDR345C",316,428,583,816,527,194,247,246,438 -"YDR346C",2636,3216,3348,4668,3776,1766,1879,1822,3058 -"YDR347W",428,507,508,590,555,1598,445,373,560 -"YDR348C",504,704,878,1411,1485,547,596,537,648 -"YDR349C",912,1000,978,1138,1328,544,572,603,1043 -"YDR350C",752,766,742,542,490,581,576,531,887 -"YDR351W",971,1126,981,1137,985,511,642,686,1037 -"YDR352W",498,601,596,585,640,316,404,449,722 -"YDR353W",1218,1552,1798,2634,3221,1449,1213,1571,1935 -"YDR354W",1043,1161,1214,863,864,559,1016,1007,1440 -"YDR356W",1145,1212,893,547,565,974,786,825,1218 -"YDR357C",1119,895,636,420,422,1272,1297,1129,1735 -"YDR358W",1393,1196,601,42,125,1344,1058,1150,1765 -"YDR359C",1203,880,582,471,599,995,1083,910,1190 -"YDR361C",526,713,960,1666,1822,118,259,294,638 -"YDR362C",610,720,592,534,719,625,538,570,913 -"YDR363W",477,529,482,525,324,283,338,321,601 -"YDR363W-A",1741,1525,1261,1004,950,1737,1773,1653,2566 -"YDR364C",488,550,516,731,669,220,275,330,586 -"YDR365C",4701,4352,3764,4281,4555,4755,4065,3094,5562 -"YDR365W-B",12,9,11,9,6,6,6,7,8 -"YDR366C",7,14,4,8,7,14,6,4,5 -"YDR367W",422,440,416,361,417,427,381,361,586 -"YDR368W",1515,1497,1197,682,284,1219,1090,1292,2069 -"YDR369C",613,666,557,278,222,344,423,441,710 -"YDR370C",468,541,481,410,597,294,384,381,577 -"YDR371W",445,489,381,218,251,383,378,359,564 -"YDR372C",1344,1423,1167,1285,1690,980,1110,1026,1672 -"YDR373W",1004,1056,854,701,736,776,859,943,1630 -"YDR374C",10,17,21,18,18,9,6,7,17 -"YDR374W-A",255,220,181,140,174,209,194,242,348 -"YDR375C",362,376,355,254,402,1662,509,397,539 -"YDR376W",404,509,498,420,482,544,370,366,539 -"YDR377W",2312,2350,1765,1242,1827,3446,3394,2997,3739 -"YDR378C",519,488,379,332,576,477,574,639,1020 -"YDR379W",985,1099,935,626,873,668,756,780,1245 -"YDR379C-A",564,435,272,114,58,665,631,650,1070 -"YDR380W",1454,1570,1312,451,119,1249,1696,1688,2136 -"YDR381W",3546,3083,2534,2757,4261,3758,3495,3293,4935 -"YDR381C-A",262,300,244,145,248,574,222,252,442 -"YDR382W",3179,3911,4243,7760,12972,829,2131,2418,4708 -"YDR383C",283,263,265,149,120,212,215,216,414 -"YDR384C",8020,6257,3372,817,672,10711,10359,8753,13233 -"YDR385W",2012,2384,2371,3696,4701,421,532,853,2059 -"YDR386W",433,478,408,224,274,425,363,366,531 -"YDR387C",575,577,460,338,426,485,344,414,685 -"YDR388W",1746,1718,1306,855,616,1734,1581,1722,2828 -"YDR389W",703,700,589,508,804,814,798,534,819 -"YDR390C",1069,1054,861,786,1128,1011,1048,972,1503 -"YDR391C",291,287,205,244,226,369,250,295,493 -"YDR392W",618,676,549,404,594,493,520,557,861 -"YDR393W",315,401,384,295,414,636,349,305,503 -"YDR394W",3982,3650,2857,1836,1792,2976,3639,3460,5814 -"YDR395W",1037,1411,1888,4302,3798,307,563,538,889 -"YDR397C",700,658,647,920,914,610,709,916,1281 -"YDR398W",413,815,2020,4231,1745,65,181,189,384 -"YDR399W",2836,3724,4636,7232,10342,1386,2260,2629,3881 -"YDR400W",200,264,266,311,454,142,120,136,238 -"YDR402C",166,127,64,39,81,255,167,149,238 -"YDR403W",125,139,110,90,96,282,166,127,195 -"YDR404C",375,370,411,460,726,400,423,385,569 -"YDR405W",590,668,519,312,529,1942,909,689,985 -"YDR406W",890,913,640,322,356,889,613,650,1014 -"YDR407C",632,673,671,500,521,420,475,434,612 -"YDR408C",438,468,475,841,1308,488,419,439,691 -"YDR409W",635,755,533,460,581,533,538,522,737 -"YDR410C",241,270,212,257,450,161,199,216,356 -"YDR411C",711,614,460,200,355,745,742,745,1062 -"YDR412W",400,577,858,1826,2238,145,251,282,491 -"YDR414C",268,304,281,270,333,222,211,208,361 -"YDR415C",414,502,463,439,492,336,389,357,542 -"YDR416W",609,664,651,723,706,292,419,423,690 -"YDR418W",3418,3896,4104,7315,10606,1130,2661,2748,4876 -"YDR419W",562,672,619,536,625,378,402,404,709 -"YDR420W",1010,1035,965,1070,842,396,513,554,953 -"YDR421W",776,832,626,464,513,584,585,564,917 -"YDR422C",983,876,685,586,753,698,745,756,1204 -"YDR423C",548,612,423,244,383,449,489,498,775 -"YDR424C",482,429,317,222,258,624,527,575,887 -"YDR425W",504,572,372,118,220,427,435,434,582 -"YDR427W",3152,3010,2261,1777,1935,2721,3046,2756,4046 -"YDR428C",348,421,406,519,545,305,303,327,526 -"YDR429C",1760,2004,2433,4141,5413,1208,1543,1384,2315 -"YDR430C",747,909,752,543,504,2601,824,644,877 -"YDR432W",2069,2966,3528,5030,3202,1049,931,1119,2137 -"YDR434W",1091,1159,941,822,932,799,812,825,1260 -"YDR435C",406,387,268,71,154,631,418,496,753 -"YDR436W",789,759,498,195,324,878,685,669,1121 -"YDR437W",82,93,66,77,94,49,50,75,127 -"YDR438W",364,350,272,243,433,399,308,312,447 -"YDR439W",289,298,295,291,338,164,212,214,333 -"YDR440W",312,357,436,302,339,190,252,268,430 -"YDR441C",708,743,881,1102,1175,334,514,521,795 -"YDR443C",766,839,672,308,326,591,585,521,825 -"YDR444W",287,321,273,304,371,406,307,279,416 -"YDR446W",1,9,4,10,8,2,12,5,8 -"YDR447C",2394,2651,2764,5066,9169,745,1846,2081,3542 -"YDR448W",322,359,379,431,457,184,224,227,357 -"YDR449C",357,567,886,1746,1498,32,149,162,323 -"YDR450W",4456,4763,5026,8272,14832,1811,3265,3448,5995 -"YDR451C",141,173,145,106,145,597,517,213,201 -"YDR452W",2557,2527,2060,1317,957,2629,2296,2121,3382 -"YDR453C",292,282,204,132,102,274,147,191,380 -"YDR454C",930,1098,1124,1881,2793,884,783,780,1445 -"YDR456W",1304,1190,928,561,691,1132,1123,1016,1684 -"YDR457W",2178,2356,2034,1758,1473,1640,1569,1543,2251 -"YDR458C",1394,1429,1291,1088,968,997,1000,1012,1587 -"YDR459C",384,423,408,395,419,273,345,335,580 -"YDR460W",446,433,413,366,573,373,428,379,604 -"YDR461W",52,40,47,38,78,49,34,39,82 -"YDR461C-A",372,325,226,104,83,375,445,535,712 -"YDR462W",342,332,285,171,330,1035,417,384,514 -"YDR463W",1631,1682,1809,2053,1811,966,1171,1204,1787 -"YDR464W",682,896,1102,1550,998,495,584,529,822 -"YDR465C",751,1239,1966,3810,3359,126,354,405,873 -"YDR466W",896,925,923,696,362,766,769,733,1143 -"YDR468C",644,684,589,625,684,634,631,611,906 -"YDR469W",319,367,428,569,490,270,305,289,428 -"YDR470C",509,540,397,184,229,847,470,493,649 -"YDR471W",3076,3584,4500,8255,11658,753,2373,2369,4075 -"YNCD0030W",3,2,2,3,4,2,2,1,3 -"YDR472W",302,350,407,508,452,172,253,229,424 -"YDR473C",707,736,635,652,739,573,642,594,937 -"YDR475C",958,916,730,500,522,772,775,739,1135 -"YDR476C",405,413,327,269,299,387,393,376,558 -"YDR477W",1593,1474,978,661,1035,1927,1429,1375,2030 -"YDR478W",141,193,198,338,233,61,94,109,168 -"YDR479C",991,817,529,358,583,980,820,800,1225 -"YDR480W",192,193,171,98,205,307,239,186,275 -"YDR481C",1344,1340,1195,912,1157,1230,1179,1346,1953 -"YDR482C",262,321,388,727,619,265,208,235,378 -"YDR483W",2363,2567,2651,3915,3452,1589,1455,1637,2785 -"YDR484W",566,484,454,321,449,377,383,416,538 -"YDR485C",995,1018,926,984,847,884,884,807,1387 -"YDR486C",985,980,857,717,664,895,814,827,1272 -"YDR487C",796,917,1001,1054,862,1221,952,903,1323 -"YDR488C",183,221,285,379,78,323,141,154,255 -"YDR489W",124,150,172,254,226,135,128,132,186 -"YDR490C",845,727,523,147,350,947,796,744,1097 -"YDR492W",658,794,878,940,725,470,544,439,642 -"YDR493W",173,209,166,179,234,635,225,193,283 -"YDR494W",773,892,641,524,792,3636,1010,829,1131 -"YDR495C",642,605,450,395,585,408,405,420,766 -"YDR496C",915,1424,2450,5710,4303,94,387,468,816 -"YDR497C",12708,11288,10671,11184,8083,21146,30051,24901,25571 -"YDR498C",453,507,478,349,396,351,452,397,599 -"YDR499W",847,844,742,444,389,509,556,586,915 -"YDR500C",2471,2750,2968,4759,7776,915,1850,2057,3620 -"YDR501W",179,182,149,170,198,162,157,121,213 -"YDR502C",4640,6548,8755,19712,10878,2883,6611,5070,6126 -"YDR503C",305,352,233,169,270,193,199,215,341 -"YDR504C",154,171,98,59,94,181,155,124,221 -"YDR505C",2251,2184,1443,615,723,2213,1816,1593,2363 -"YDR506C",481,486,402,227,115,274,285,296,563 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-"YDR527W",476,773,1696,2280,735,123,240,277,506 -"YNCD0032C",44,41,52,44,57,21,39,28,48 -"YDR528W",259,359,427,431,763,73,148,164,281 -"YDR529C",4382,4061,3064,2205,4029,9141,7629,5881,7069 -"YDR530C",364,439,356,326,380,440,385,357,556 -"YDR531W",1696,1796,1552,1609,1067,790,1300,1354,2001 -"YDR532C",398,419,363,321,540,412,364,331,542 -"YDR533C",2275,2409,1604,990,645,543,588,959,2523 -"YDR534C",233,157,90,37,155,309,264,265,293 -"YDR536W",1021,844,412,73,163,1602,1316,1925,1931 -"YDR538W",359,352,230,174,262,177,225,296,505 -"YDR539W",342,292,252,205,310,401,290,317,484 -"YDR540C",28,15,27,33,56,48,31,34,41 -"YDR541C",232,300,251,289,300,191,171,177,360 -"YEL077C",129,125,115,87,150,81,82,108,181 -"YEL073C",345,323,286,200,301,595,572,489,699 -"YEL072W",201,342,399,672,432,169,170,178,280 -"YEL071W",2004,2751,4217,4587,3336,1891,2233,1423,2408 -"YEL070W",51,51,24,6,16,68,43,63,74 -"YEL069C",14,24,18,8,17,34,7,20,24 -"YEL068C",165,183,172,143,118,239,239,168,274 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-"YEL012W",1605,1455,975,190,409,1550,1637,1655,2618 -"YEL011W",7833,5773,2523,103,551,9324,6467,7188,11443 -"YEL009C-A",22,4,7,6,8,23,9,6,17 -"YEL009C",27370,23805,19814,21250,23648,17432,25826,24988,40088 -"YEL008W",35,26,20,4,12,38,39,26,50 -"YEL007W",1759,1399,1104,1018,2298,1652,1459,1267,1789 -"YEL006W",665,725,717,779,759,456,504,506,817 -"YEL005C",425,441,295,152,126,355,321,373,595 -"YEL004W",381,362,285,210,206,227,241,263,448 -"YEL003W",517,565,510,695,969,320,435,431,714 -"YEL002C",2198,2248,2001,1820,1685,1507,1618,1783,2816 -"YEL001C",872,983,942,1039,1465,866,767,748,1173 -"YER001W",679,1011,1180,1772,1156,254,292,355,621 -"YER002W",896,1188,1713,3280,3067,262,600,742,1214 -"YER003C",874,1005,853,782,820,660,598,741,1169 -"YER004W",5498,4820,3528,1933,1126,4397,5081,5144,8613 -"YER005W",582,620,631,865,916,395,370,385,667 -"YER006W",1207,1760,2623,5872,6115,202,546,537,1091 -"YER007W",352,325,359,342,368,290,239,232,383 -"YER007C-A",786,822,851,1147,1411,418,601,719,1116 -"YNCE0011C",14,11,12,10,5,9,3,10,14 -"YER008C",960,1031,974,994,766,660,657,634,1090 -"YER009W",1337,1495,1314,1645,2725,1353,1345,1415,2033 -"YER010C",1284,1292,977,588,536,1279,1171,1217,2012 -"YER011W",29,19,18,11,19,71,29,23,45 -"YER012W",2903,2865,2225,1732,1559,2439,2862,2681,4183 -"YER013W",470,544,542,621,521,235,319,326,616 -"YER014W",592,638,650,587,186,460,466,534,837 -"YER015W",4891,4697,3145,563,167,11855,6112,4574,6378 -"YER016W",330,388,410,415,537,331,321,314,472 -"YER017C",1300,1211,889,682,1065,2224,1179,1233,1710 -"YER018C",217,207,200,162,277,390,270,241,398 -"YER019W",451,495,435,340,457,475,448,447,714 -"YER019C-A",1165,1031,909,929,1383,1131,1221,1311,1973 -"YER020W",1797,1576,1147,603,956,1765,1410,1662,2718 -"YER021W",5239,5039,3662,2652,2695,4141,4462,4424,6709 -"YER022W",848,864,790,663,702,555,569,575,997 -"YER023W",1626,1514,1347,1305,1013,1847,1683,1773,2659 -"YER024W",5020,4472,3314,974,1427,8872,12120,7411,8699 -"YER025W",2279,2765,2864,4543,5069,1207,1727,1639,2689 -"YER026C",2393,2270,1880,1178,1162,4708,3941,3538,4126 -"YER027C",522,622,500,339,343,555,432,403,635 -"YER028C",84,92,90,63,28,49,49,53,124 -"YER029C",526,550,598,721,875,485,517,554,825 -"YER030W",2516,2289,2000,1377,1131,3118,2814,2475,3881 -"YER031C",816,919,693,708,878,778,960,893,1402 -"YER032W",367,469,435,396,299,450,398,259,419 -"YER033C",390,425,335,315,264,318,252,257,402 -"YER034W",366,337,334,303,268,244,355,384,609 -"YER035W",605,539,535,382,226,364,396,488,883 -"YER036C",2397,3561,5734,11910,5578,439,780,1089,2426 -"YER037W",486,522,508,443,228,265,263,348,626 -"YER038C",287,320,328,332,275,124,170,185,348 -"YER039C",251,213,171,69,56,167,192,218,377 -"YER039C-A",162,162,116,41,29,162,147,153,301 -"YER040W",645,724,632,602,548,333,404,392,557 -"YER041W",387,445,443,331,234,311,334,292,524 -"YER042W",1967,2124,1655,1593,1264,1452,1362,1661,2869 -"YER043C",2678,4151,6971,14450,9587,3209,3243,2504,3099 -"YER044C",1108,1042,734,469,476,2106,1354,1260,1805 -"YER044C-A",22,27,40,67,49,24,7,8,18 -"YER045C",255,294,459,624,605,217,155,212,315 -"YER046W",278,270,211,102,214,227,265,283,495 -"YER047C",771,905,765,713,709,640,675,625,956 -"YER048C",1675,1637,1323,1146,1293,2447,1719,1553,2316 -"YER048W-A",461,446,374,303,374,1199,543,469,648 -"YER049W",887,1251,1939,4128,3561,297,535,514,866 -"YER050C",523,533,465,401,601,1728,688,540,787 -"YER051W",533,558,414,305,368,331,383,409,642 -"YER052C",2925,2813,3683,5884,2056,343,1487,1476,3083 -"YER053C",1216,818,394,101,206,2177,985,1095,2013 -"YER053C-A",8510,4964,1771,515,1281,6126,7286,7060,10297 -"YER054C",5863,3758,1423,58,83,9871,5170,5525,9235 -"YER055C",2411,2731,3088,5522,6139,2392,2065,1920,3258 -"YER056C",2571,4575,10135,19583,10323,313,1108,1448,2500 -"YER056C-A",1415,1746,2063,3951,5164,281,808,775,1670 -"YER057C",1437,1390,1232,1254,1149,1311,1072,1173,1895 -"YER058W",240,219,170,122,138,1479,332,282,348 -"YER059W",578,542,420,196,274,388,483,515,778 -"YER060W",494,536,589,894,735,245,290,305,485 -"YER060W-A",271,361,443,637,437,133,131,183,259 -"YER061C",341,502,643,1009,415,170,140,175,303 -"YER062C",625,1330,4291,9256,1478,169,272,352,672 -"YER063W",564,675,596,569,519,515,525,565,872 -"YER064C",222,387,765,465,408,71,132,114,224 -"YER065C",1914,1957,1478,785,809,1933,2631,1913,3051 -"YNCE0015C",3,15,7,5,5,5,5,6,9 -"YER066W",257,292,192,90,112,343,295,304,441 -"YER067W",761,375,125,34,210,5226,889,2731,2721 -"YER068W",754,844,841,868,1090,569,770,617,901 -"YER069W",6500,5321,4666,7699,5692,1021,3717,3615,6808 -"YER070W",908,1310,1121,1022,2946,624,420,521,891 -"YER071C",228,257,194,176,225,305,254,227,377 -"YER072W",599,667,650,756,961,359,461,451,703 -"YER073W",2069,2675,4324,9510,2840,375,1028,1095,2120 -"YER074W",2784,3098,3248,5133,9063,859,2031,2276,4367 -"YER074W-A",505,547,406,362,468,466,471,485,796 -"YER075C",867,987,973,917,929,604,477,625,999 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-"YLR058C",2072,3348,5091,21530,13011,691,583,788,1782 -"YLR059C",217,245,292,510,406,276,348,265,371 -"YLR060W",1180,1514,2094,4104,4484,611,1118,926,1351 -"YLR061W",1847,2313,2756,5212,7297,400,1181,1241,2507 -"YLR063W",138,221,462,737,221,13,48,57,95 -"YLR064W",822,897,844,748,636,557,516,566,1015 -"YLR065C",521,648,614,826,1058,265,389,415,720 -"YLR066W",672,647,545,515,593,472,641,598,932 -"YLR067C",265,336,353,399,355,333,268,196,276 -"YLR068W",274,349,521,1083,1058,59,138,130,267 -"YLR069C",855,899,828,674,1001,6435,1194,829,1196 -"YLR070C",913,788,527,98,32,1389,842,878,1441 -"YLR071C",667,820,817,871,985,485,518,440,723 -"YLR072W",855,835,694,425,427,539,660,703,983 -"YLR073C",112,196,390,818,462,22,45,64,109 -"YLR074C",342,556,1225,2788,1470,94,192,244,441 -"YLR075W",19502,21600,21284,30448,46818,6256,12518,14604,26334 -"YLR077W",750,812,716,515,357,965,650,611,1021 -"YLR078C",478,546,449,425,584,374,431,514,767 -"YLR079W",645,604,516,401,526,441,801,1371,1354 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-"YLR168C",416,553,626,820,1931,470,632,427,680 -"YLR170C",441,442,396,289,393,387,503,547,812 -"YLR172C",761,806,868,1438,1646,283,472,521,909 -"YLR173W",724,692,653,470,324,341,482,538,837 -"YLR174W",6604,6317,4138,1182,475,7828,10930,8874,11179 -"YLR175W",1734,2809,4521,11273,10769,235,842,875,1666 -"YLR176C",155,169,196,263,388,112,135,91,150 -"YLR177W",603,502,269,97,368,1138,474,610,965 -"YLR178C",2941,2291,1356,311,119,3828,2393,2879,4929 -"YLR179C",311,433,624,1730,1979,397,273,326,479 -"YLR180W",828,1889,4237,14065,7613,215,504,494,849 -"YLR181C",959,1016,846,544,433,1096,1019,915,1310 -"YLR182W",782,838,680,620,787,1170,911,733,985 -"YLR183C",220,228,220,146,349,229,173,191,271 -"YLR185W",1865,2251,2216,4061,5643,392,989,1170,2117 -"YLR186W",388,644,879,1704,1883,77,330,323,527 -"YLR187W",303,303,286,307,325,122,161,166,261 -"YLR188W",947,1038,943,852,797,692,764,743,1179 -"YLR189C",2134,2108,1437,753,828,1691,1411,1444,2440 -"YLR190W",757,755,656,527,646,1354,2181,1190,1089 -"YLR191W",413,515,427,406,468,498,423,391,656 -"YLR192C",1547,1589,1422,1671,2096,1004,1199,1284,2207 -"YLR193C",728,675,638,440,582,1121,794,670,1013 -"YLR194C",1073,790,732,752,1094,555,1070,2100,2442 -"YLR195C",677,774,733,885,996,570,533,534,767 -"YLR196W",841,1386,2304,5501,4782,98,446,458,810 -"YLR197W",1612,2774,4318,10425,12853,292,821,795,1462 -"YLR199C",863,903,752,696,609,523,705,604,1159 -"YLR200W",416,470,582,765,714,266,337,322,569 -"YLR201C",719,677,511,318,271,884,645,625,903 -"YLR203C",640,776,539,447,659,2211,679,556,772 -"YLR204W",464,504,381,253,448,2074,629,583,754 -"YLR205C",624,631,464,150,260,1847,2462,1239,1253 -"YLR206W",1836,1620,1220,673,1166,2437,1851,1590,2429 -"YLR207W",495,499,478,350,322,391,361,360,555 -"YLR208W",1976,2093,1920,1850,1753,1850,2019,1792,2858 -"YLR209C",317,339,292,332,361,481,343,324,434 -"YLR210W",302,316,362,403,373,249,288,212,376 -"YLR211C",604,539,391,209,143,362,498,424,728 -"YLR212C",432,512,452,340,535,313,416,442,609 -"YLR213C",129,110,99,114,130,199,141,143,182 -"YLR214W",292,317,249,254,247,273,230,216,386 -"YLR215C",327,414,468,665,600,156,213,243,396 -"YLR216C",6287,5434,3937,1911,798,5161,4128,4813,9567 -"YLR218C",178,155,80,22,53,583,243,217,312 -"YLR219W",2208,2034,1406,340,420,1601,1501,1498,2447 -"YLR220W",2014,1972,1706,1339,1959,1327,1663,1720,2779 -"YLR221C",425,577,740,1583,1885,186,310,310,532 -"YLR222C",508,839,1391,3040,2123,32,196,190,348 -"YLR223C",708,1111,2491,4729,976,180,404,408,795 -"YLR224W",545,756,1178,1356,805,206,293,341,620 -"YLR225C",711,725,673,472,556,496,537,531,971 -"YLR226W",274,382,651,907,378,114,177,165,249 -"YLR227C",393,345,401,462,426,589,597,373,540 -"YNCL0032C",54,63,28,15,29,90,92,59,99 -"YLR227W-B",298,303,245,260,135,160,147,120,186 -"YLR228C",779,607,384,211,448,988,791,714,1096 -"YLR229C",1100,1190,1213,1237,1899,1468,1276,1202,1773 -"YLR231C",1528,1625,1453,1121,963,1162,1042,1304,2113 -"YLR233C",497,515,392,246,310,292,317,388,596 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-"YLR256W",2710,2336,1872,1237,1403,1167,1616,1811,2825 -"YLR256W-A",13,12,17,12,14,15,5,9,15 -"YLR257W",2973,2976,2014,1608,2373,2709,1793,2316,4053 -"YLR258W",2351,1618,800,180,156,3746,1670,2584,4075 -"YLR259C",9483,7693,5281,2382,2995,23725,8309,7155,13083 -"YLR260W",657,687,629,534,461,411,419,462,743 -"YLR261C",2,5,6,1,5,10,4,5,3 -"YLR262C",287,326,273,268,299,222,272,236,396 -"YLR262C-A",954,921,819,1033,1690,712,904,969,1619 -"YLR263W",383,432,338,428,385,184,201,212,391 -"YLR264W",1012,1187,1227,2071,3068,362,947,965,1679 -"YLR264C-A",598,646,679,1256,1997,175,453,418,699 -"YLR265C",502,453,300,177,217,380,347,418,720 -"YLR266C",668,637,453,253,507,500,543,557,832 -"YLR267W",644,669,352,70,131,531,469,510,793 -"YLR268W",637,692,655,667,719,699,668,623,954 -"YLR270W",2188,1859,1096,270,231,2347,1678,1778,2823 -"YLR271W",471,426,319,185,105,386,316,335,624 -"YLR272C",543,632,578,684,799,457,471,354,651 -"YLR273C",1239,1222,940,459,593,551,890,1224,1670 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-"YPR111W",743,770,668,523,528,473,591,507,784 -"YPR112C",707,1086,1691,3721,3110,84,371,417,713 -"YPR113W",373,523,636,1306,1935,672,326,338,493 -"YPR114W",412,522,582,1012,926,479,383,328,517 -"YPR115W",1541,1541,1132,557,534,1344,1130,1103,1711 -"YPR116W",45,53,80,79,16,8,11,13,30 -"YPR117W",954,1044,918,723,651,570,603,590,967 -"YPR118W",1159,1407,1314,1519,1229,761,1128,1040,1486 -"YPR119W",137,147,104,108,151,438,664,308,227 -"YPR120C",264,283,236,184,428,162,187,236,406 -"YPR121W",352,349,293,261,299,312,276,264,430 -"YPR122W",1157,1179,991,1178,1270,1002,817,767,1235 -"YPR124W",189,237,288,362,346,361,172,165,293 -"YPR125W",730,1069,1783,2950,1113,466,540,532,815 -"YPR127W",3005,2671,1818,959,306,1147,730,1157,3392 -"YPR128C",1485,1396,1199,1105,1048,734,903,1076,1889 -"YPR129W",902,1004,899,803,836,906,903,727,1127 -"YPR131C",384,358,357,354,421,239,254,293,447 -"YPR132W",3543,3626,3681,5554,10411,1434,2855,3152,5675 -"YPR133C",1899,1984,1927,1891,1945,1171,1599,1673,2512 -"YPR133W-A",205,250,235,258,274,727,283,193,331 -"YPR134W",521,569,441,311,407,580,442,501,834 -"YPR135W",842,885,713,372,524,527,542,614,1079 -"YPR137W",591,922,1697,3753,2051,215,384,355,638 -"YNCP0019W",82,72,43,25,8,43,47,40,74 -"YPR138C",2588,2274,1587,1538,2356,1630,2047,1453,2520 -"YPR139C",553,671,684,793,605,366,448,500,793 -"YPR140W",627,724,702,646,604,1208,684,573,980 -"YPR141C",420,446,433,424,555,463,429,330,428 -"YPR143W",781,1054,1318,2418,3061,260,587,664,1036 -"YPR144C",360,576,1118,2211,1382,49,181,177,337 -"YPR145W",4055,5313,6899,14077,16750,741,2638,2245,4128 -"YPR145C-A",98,95,70,92,110,85,58,92,131 -"YPR147C",374,407,372,273,270,424,346,333,476 -"YPR148C",2743,2689,2144,1296,1090,2764,2371,2654,4219 -"YPR149W",41323,28085,14100,3208,859,54048,44101,40923,66810 -"YPR151C",2639,1917,984,86,94,6982,7182,4616,5354 -"YPR152C",246,281,353,443,231,154,220,225,398 -"YPR153W",85,120,129,143,94,37,40,38,80 -"YPR154W",1320,1173,1045,600,615,1001,910,799,1194 -"YPR155C",1466,1378,917,232,391,1841,1473,1318,1921 -"YPR156C",501,499,401,352,278,576,828,603,719 -"YPR157W",86,64,57,104,68,110,137,91,120 -"YPR158W",1174,980,548,78,171,768,783,942,1684 -"YPR158W-B",20,14,7,14,6,19,5,9,15 -"YPR159W",1046,1638,2209,4289,4445,599,870,737,1072 -"YPR160W",9015,6285,3226,733,175,25124,6862,9317,12504 -"YPR161C",625,732,778,938,963,357,562,507,807 -"YPR162C",372,413,383,442,439,208,199,256,401 -"YPR163C",3132,3740,4426,8747,11744,1505,2687,2387,3903 -"YPR164W",1167,1263,1151,823,297,491,609,678,1041 -"YPR165W",5069,4707,3593,3136,4010,6328,5034,4790,7574 -"YPR166C",248,252,195,181,259,963,274,264,355 -"YPR167C",876,1317,1712,3663,2065,277,554,577,995 -"YPR168W",270,322,288,338,148,106,199,203,311 -"YPR169W",1283,1605,1660,2602,2060,635,997,933,1705 -"YPR170W-B",669,679,569,614,896,898,872,839,1259 -"YPR171W",404,440,497,461,522,290,305,291,454 -"YPR172W",852,740,465,158,158,719,617,628,1095 -"YPR173C",1880,1848,1684,1654,2052,1531,1778,1794,2937 -"YPR174C",263,281,250,152,179,176,176,240,475 -"YPR175W",142,202,197,218,563,142,112,125,184 -"YPR176C",576,572,537,436,627,663,522,574,893 -"YPR178W",512,547,527,424,570,451,472,478,772 -"YPR179C",735,728,598,535,629,517,571,492,904 -"YPR180W",609,672,541,489,528,566,545,517,831 -"YPR181C",2305,2530,2400,2571,1976,2120,2106,1893,2732 -"YPR182W",465,365,301,168,213,859,897,733,1023 -"YPR183W",814,894,944,1127,1284,663,561,636,1209 -"YPR184W",2922,2308,1220,175,156,4390,2166,2372,3765 -"YPR185W",1044,934,655,307,295,947,886,819,1289 -"YPR186C",223,320,428,575,408,96,146,122,226 -"YPR187W",1153,1450,1758,3134,3794,524,1085,960,1483 -"YPR188C",552,566,527,510,545,512,522,472,798 -"YPR189W",972,1064,1044,1266,1023,586,656,620,951 -"YPR190C",423,672,1026,1904,1522,117,335,276,400 -"YPR191W",2083,2130,1861,1286,2188,3498,3289,2218,3104 -"YPR192W",938,876,532,115,179,553,688,654,1240 -"YPR193C",429,385,255,102,33,234,314,290,505 -"YPR194C",275,283,261,183,147,119,141,135,235 -"YPR195C",47,43,47,21,42,54,55,37,51 -"YPR196W",281,320,294,281,381,219,222,238,350 -"YPR198W",682,656,617,593,549,443,477,528,792 -"YPR199C",456,463,441,392,436,386,423,408,709 -"YPR200C",60,56,24,29,49,68,53,60,74 -"YPR201W",171,178,136,67,84,133,137,165,222 -"YPR202W",6,10,8,3,11,4,4,2,3 -"YPR204W",57,60,65,36,73,59,42,41,68 -"Q0020",39,24,27,19,34,52,74,43,83 -"Q0055",1,11,7,7,3,11,15,12,24 -"Q0050",3,6,2,2,7,4,17,7,12 -"Q0130",1,3,3,2,1,3,3,4,7 -"Q0158",156,148,92,98,149,195,313,188,425 diff --git a/test_data/YMC/samplesheet_RCvsOX.csv b/test_data/YMC/samplesheet_RCvsOX.csv deleted file mode 100644 index 9748bc2b..00000000 --- a/test_data/YMC/samplesheet_RCvsOX.csv +++ /dev/null @@ -1,10 +0,0 @@ -"sample","fase" -"Time.1","RC" -"Time.2","RC" -"Time.3","OX" -"Time.4","OX" -"Time.5","OX" -"Time.13","RC" -"Time.14","RC" -"Time.15","RC" -"Time.16","RC" From a2d382449296bd52bd2d1dee26f89d20ce2e0cc9 Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 15:47:56 +0200 Subject: [PATCH 10/15] solve remaining lint erros --- conf/crg.config | 2 +- subworkflows/local/experimental/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/crg.config b/conf/crg.config index 29d4366e..d1f6b419 100644 --- a/conf/crg.config +++ b/conf/crg.config @@ -18,7 +18,7 @@ process { cpus = { check_max( 2 , 'cpus' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } - } + } withLabel:process_medium{ queue = 'cn-el7,short-centos79' cpus = { check_max( 6 , 'cpus' ) } diff --git a/subworkflows/local/experimental/main.nf b/subworkflows/local/experimental/main.nf index 62d51241..6e811027 100644 --- a/subworkflows/local/experimental/main.nf +++ b/subworkflows/local/experimental/main.nf @@ -70,4 +70,4 @@ workflow EXPERIMENTAL { emit: output = ch_out -} \ No newline at end of file +} From b59f668d53fe48e477def7d0e392b39b4d4b9202 Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 15:54:12 +0200 Subject: [PATCH 11/15] update propr/grea with nf-core modules install --- modules/nf-core/propr/grea/main.nf | 4 ++-- modules/nf-core/propr/grea/templates/grea.R | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/propr/grea/main.nf b/modules/nf-core/propr/grea/main.nf index 66cf3c05..d2e1ee6d 100644 --- a/modules/nf-core/propr/grea/main.nf +++ b/modules/nf-core/propr/grea/main.nf @@ -1,11 +1,11 @@ process PROPR_GREA { tag "$meta.id" - label 'process_high' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-propr:5.0.4': - 'quay.io/biocontainers/r-propr:5.0.4' }" + 'biocontainers/r-propr:5.0.4' }" input: tuple val(meta), path(adj) diff --git a/modules/nf-core/propr/grea/templates/grea.R b/modules/nf-core/propr/grea/templates/grea.R index 6e1c6a00..2d568b70 100644 --- a/modules/nf-core/propr/grea/templates/grea.R +++ b/modules/nf-core/propr/grea/templates/grea.R @@ -122,8 +122,8 @@ add_missing <- function(adjacency_matrix, knowledge_matrix){ opt <- list( adj = '$adj', gmt = '$gmt', - prefix = ifelse('$task.ext.prefix' == 'null', '$meta.pathway_name', '$task.ext.prefix'), - permutation = 10, + prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix'), + permutation = 100, fixseed = TRUE, ncores = as.integer('$task.cpus') ) @@ -214,7 +214,7 @@ write.table( G, file = paste0(opt\$prefix, '.go.tsv'), col.names = TRUE, - row.names = TRUE, # False + row.names = TRUE, sep = '\\t', quote = FALSE From 45b776ec8903346be9cee588d049c5795e9c3b2f Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 16:34:09 +0200 Subject: [PATCH 12/15] modify propr main.nf to match nf-core repository --- modules/nf-core/propr/propr/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/propr/propr/main.nf b/modules/nf-core/propr/propr/main.nf index 531e575c..111f6d58 100644 --- a/modules/nf-core/propr/propr/main.nf +++ b/modules/nf-core/propr/propr/main.nf @@ -5,7 +5,7 @@ process PROPR_PROPR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-propr:5.0.3': - 'quay.io/biocontainers/r-propr:5.0.3' }" + 'biocontainers/r-propr:5.0.3' }" input: tuple val(meta), path(count) From d60f031d2389c19de37fa201d9b472f19e416276 Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 16:37:50 +0200 Subject: [PATCH 13/15] install propd with nf-core modules install --- modules/nf-core/propr/propd/main.nf | 2 +- modules/nf-core/propr/propd/meta.yml | 10 +++++++++- modules/nf-core/propr/propd/templates/propd.R | 10 +++++----- .../propr/propd/tests/main.nf.test.snap | 18 +++++++++--------- 4 files changed, 24 insertions(+), 16 deletions(-) diff --git a/modules/nf-core/propr/propd/main.nf b/modules/nf-core/propr/propd/main.nf index d7ada4ab..ba7727d0 100644 --- a/modules/nf-core/propr/propd/main.nf +++ b/modules/nf-core/propr/propd/main.nf @@ -5,7 +5,7 @@ process PROPR_PROPD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-propr:5.0.3': - 'quay.io/biocontainers/r-propr:5.0.3' }" + 'biocontainers/r-propr:5.0.3' }" input: tuple val(meta), path(count) diff --git a/modules/nf-core/propr/propd/meta.yml b/modules/nf-core/propr/propd/meta.yml index 1c408d73..7dcb4625 100644 --- a/modules/nf-core/propr/propd/meta.yml +++ b/modules/nf-core/propr/propd/meta.yml @@ -52,8 +52,16 @@ output: pattern: "*.propd.tsv" - fdr: type: file - description: (optional) propr fdr table + description: (optional) propd fdr table pattern: "*.fdr.tsv" + - adj: + type: file + description: (optional) propd adj table + pattern: "*.adj.csv" + - warnings: + type: file + description: propd warnings + pattern: "*.warnings.txt" - session_info: type: file description: dump of R SessionInfo diff --git a/modules/nf-core/propr/propd/templates/propd.R b/modules/nf-core/propr/propd/templates/propd.R index 1bdae252..63dbed49 100644 --- a/modules/nf-core/propr/propd/templates/propd.R +++ b/modules/nf-core/propr/propd/templates/propd.R @@ -66,7 +66,7 @@ read_delim_flexible <- function(file, header = TRUE, row.names = 1, check.names #' Extract the values for a single metric and convert it into a genes x genes matrix. #' #' @param object propd object -one_metric_df <- function(object) { +one_metric_df <- function(object){ results <- getResults(object) #keep only the metric of interest one_metric <- cbind(results\$Partner, results\$Pair, results\$theta) @@ -138,7 +138,7 @@ convert_to_adjacency <- function(matrix, cutoff) { ################################################ opt <- list( - prefix = ifelse('$task.ext.prefix' == 'null','$meta.pathway_name', '$task.ext.prefix'), + prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix'), count = '$count', samplesheet = '$samplesheet', features_id_col = 'gene_id', # column name of feature ids @@ -147,9 +147,9 @@ opt <- list( metric = 'theta_d', # differential proportionality metric: theta_d, theta_e or theta_f alpha = NA, # alpha for boxcox transformation permutation = 0, # permutation cycles for computing FDR - cutoff_min = 0.05, # minimun threshold to test - cutoff_max = 0.95, # maximun threshold to test - cutoff_interval = 0.05, # interval between thresholds + cutoff_min = NA, # minimun threshold to test + cutoff_max = NA, # maximun threshold to test + cutoff_interval = NA, # interval between thresholds fixseed = FALSE, adjacency = FALSE, fdrVal = 0.05, diff --git a/modules/nf-core/propr/propd/tests/main.nf.test.snap b/modules/nf-core/propr/propd/tests/main.nf.test.snap index 58199b4b..e0291044 100644 --- a/modules/nf-core/propr/propd/tests/main.nf.test.snap +++ b/modules/nf-core/propr/propd/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-16T11:55:35.703293" + "timestamp": "2024-05-23T13:10:06.778954" }, "Test propr/propd using theta_e and boxcox permutation - results": { "content": [ @@ -31,7 +31,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-16T11:59:33.28078" + "timestamp": "2024-05-23T13:13:35.158486" }, "Test propr/propd using theta_e permutation - results": { "content": [ @@ -48,7 +48,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-16T11:57:24.038188" + "timestamp": "2024-05-23T13:12:03.500722" }, "versions": { "content": [ @@ -60,7 +60,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-16T11:53:45.165637" + "timestamp": "2024-05-23T13:07:07.588326" }, " - results": { "content": [ @@ -77,7 +77,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-16T14:13:47.602525" + "timestamp": "2024-05-23T13:16:44.428551" }, " Test propr/propd using default boxcox permutation - results": { "content": [ @@ -94,7 +94,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-16T11:55:32.476341" + "timestamp": "2024-05-23T13:10:02.25738" }, "Test propr/propd using default permutation - results": { "content": [ @@ -111,7 +111,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-16T11:53:43.056295" + "timestamp": "2024-05-23T13:07:04.720183" }, "Test propr/propd with adjacency matrix - adj": { "content": [ @@ -120,7 +120,7 @@ { "id": "test" }, - "test.adj.csv:md5,f9d19255f9400e6c4daa01f86d74f017" + "test.adj.csv:md5,9da907136fba72b0e098c7fbacbeb837" ] ] ], @@ -128,6 +128,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-16T14:13:47.427246" + "timestamp": "2024-05-23T13:16:38.527389" } } \ No newline at end of file From 8b2535174b225e1fd0325403beeb29c9fcefbd20 Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 16:47:30 +0200 Subject: [PATCH 14/15] fix pre-commit errors in .json files --- assets/schema_tools.json | 2 +- nextflow_schema_coda.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/schema_tools.json b/assets/schema_tools.json index 4119c58e..1820b94e 100644 --- a/assets/schema_tools.json +++ b/assets/schema_tools.json @@ -46,7 +46,7 @@ "type": "string", "meta": ["args_enr_cor"] }, - "sel_method":{ + "sel_method": { "type": "string", "meta": ["sel_method"], "errorMessage": "choose filtervar or none" diff --git a/nextflow_schema_coda.json b/nextflow_schema_coda.json index 76b4f1dd..cba300f4 100644 --- a/nextflow_schema_coda.json +++ b/nextflow_schema_coda.json @@ -22,4 +22,4 @@ } } } -} \ No newline at end of file +} From fc123ec0b72b7ef13c8bc7c7b982dfaa3d29077f Mon Sep 17 00:00:00 2001 From: Cristina Araiz Date: Thu, 18 Jul 2024 16:52:17 +0200 Subject: [PATCH 15/15] install propr/propr with nf-core modules install --- modules.json | 2 +- modules/nf-core/propr/propr/templates/propr.R | 35 +------------------ 2 files changed, 2 insertions(+), 35 deletions(-) diff --git a/modules.json b/modules.json index d4e06ef3..c4aa0ba5 100644 --- a/modules.json +++ b/modules.json @@ -77,7 +77,7 @@ }, "propr/propr": { "branch": "master", - "git_sha": "c8b064f86eaa6c7ca89286bc12c0e517be0e6215", + "git_sha": "132fa6c9bd2515807f6a1cdec1ad7d03c817bcc9", "installed_by": ["modules"] }, "proteus/readproteingroups": { diff --git a/modules/nf-core/propr/propr/templates/propr.R b/modules/nf-core/propr/propr/templates/propr.R index 1f8c6769..a9dbd7bd 100644 --- a/modules/nf-core/propr/propr/templates/propr.R +++ b/modules/nf-core/propr/propr/templates/propr.R @@ -121,39 +121,6 @@ seqCutoff <- function(object){ #' @param metric Metric used to calculate the proportionality values. Options are 'cor', 'rho', 'phi', 'phs', 'vlr', 'pcor', 'pcor.shrink', 'pcor.bshrink' #' #' @return cutoff value. Proportionality values higher than this cutoff are considered significant. -# valCutoff <- function(object, metric, fdrVal = 0.05){ -# fdr_df <- object@fdr -# print(fdr_df) -# metric_up <- c("rho", "cor", "pcor", "pcor.shrink", "pcor.bshrink") -# if (prod(dim(fdr_df) == 0)){ -# warning("Please run updateCutoff on propr first") -# }else{ -# fdr_vals <- fdr_df\$FDR -# if (any(is.na(fdr_vals))){ -# stop("FDR not defined. This metric is not appropiate for the given dataset") -# } -# threshold <- any(fdr_vals <= fdrVal) -# if (metric %in% metric_up){ -# if (threshold){ -# fdr_threshold <- fdr_vals[which.max(fdr_vals <= fdrVal)] -# }else{ -# warning("FDR is higher than the specified threshold for all proportionality values. Using the lowest fdr instead") -# fdr_threshold <- fdr_vals[length(fdr_vals)] -# } -# }else{ -# if (threshold){ -# fdr_threshold <- fdr_vals[which.min(fdr_vals <= fdrVal) - 1] -# }else{ -# warning("FDR is higher than the specified threshold for all proportionality values. Using the lowest fdr instead") -# fdr_threshold <- fdr_vals[1] -# } -# } -# cutoff <- fdr_df\$cutoff[fdr_df\$FDR == fdr_threshold] -# } -# return(cutoff) -# } - - valCutoff <- function(object, metric, fdrVal = 0.05){ fdr_df <- object@fdr print(fdr_df) @@ -203,7 +170,7 @@ convert_to_adjacency <- function(matrix, cutoff, metric) { opt <- list( count = '$count', - prefix = ifelse('$task.ext.prefix' == 'null', '$meta.pathway_name', '$task.ext.prefix'), + prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix'), transformation = 'clr', reference = NA, alpha = NA,