nf-core · mribeirodantas · May 24, 2024 · May 24, 2024 · May 26, 2024 · May 26, 2024
diff --git a/modules/nf-core/rtn/tna/environment.yml b/modules/nf-core/rtn/tna/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-rtn=2.30.0
diff --git a/modules/nf-core/rtn/tna/main.nf b/modules/nf-core/rtn/tna/main.nf
@@ -0,0 +1,50 @@
+process RTN_TNA {
    debug true
+    tag "{$tni_object.name}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+	'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/96/96979cd0715edeb5d68ebbd19a353760298ebf53bf729d3b68764b2bb00683f7/data':
+        'community.wave.seqera.io/library/bioconductor-rtn:2.30.0--71b797cd8b2d56b3' }"
+
+    input:
+    tuple val(meta), path(tni_object)
+    tuple val(meta), path(degs)
+    tuple val(meta), path(degs_log2)
+    tuple val(meta), path(degs_annotation)
+
+    output:
+    tuple val(meta), path("tna.rds")               , emit: tna_object
+    tuple val(meta), path("mra.rds")               , emit: mra_object
+    tuple val(meta), path("gsea1.rds")             , emit: gsea1_object
+    tuple val(meta), path("gsea1_plot.pdf")        , emit: gsea1_plot
+    tuple val(meta), path("gsea2.rds")             , emit: gsea2_object
+    tuple val(meta), path("gsea2_plot.pdf")        , emit: gsea2_plot
+    path "versions.yml"                            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    template 'rtn_tna.r'
+
+    stub:
+    def args = task.ext.args ?: ''
+
+    """
+    touch tna.rds
+    touch mra.rds
+    touch gsea1.rds
+    touch gsea1_plot.pdf
+    touch gsea2.rds
+    touch gsea2_plot.pdf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bioconductor-rtn: \$(Rscript -e "suppressWarnings(library(RTN)); cat(as.character(packageVersion('RTN')))")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/rtn/tna/meta.yml b/modules/nf-core/rtn/tna/meta.yml
@@ -0,0 +1,120 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "rtn_tna"
+description: Uses the RTN R package for transcription network analysis (TNA)
+keywords:
+  - regulatory network
+  - transcriptomics
+  - transcription factors
+tools:
+  - "rtn":
+      description: "RTN: Reconstruction of Transcriptional regulatory Networks and analysis
+        of regulons"
+      homepage: "https://www.bioconductor.org/packages/release/bioc/html/RTN.html"
+      documentation: "https://www.bioconductor.org/packages/release/bioc/vignettes/RTN/inst/doc/RTN.html"
+      tool_dev_url: "https://www.bioconductor.org/packages/release/bioc/html/RTN.html"
+      doi: "10.1038/ncomms3464"
+      licence: ["Artistic-2.0"]
+      identifier: biotools:rtn
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - tni_object:
+        type: file
+        description: TNI object from the RTN R package
+        pattern: "*.rds"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - degs:
+        type: file
+        description: TSV file with DEGs names
+        pattern: "*.tsv"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - degs_log2:
+        type: file
+        description: A TSV with genes and differential expression levels (usually in
+          log2)
+        pattern: "*.tsv"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - degs_annotation:
+        type: file
+        description: An optional TSV with gene anottation mapped to the DEGs
+        pattern: "*.tsv"
+output:
+  - tna_object:
+      - meta:
+          type: file
+          description: RDS R Object with the TNA object
+          pattern: "tna.rds"
+      - tna.rds:
+          type: file
+          description: RDS R Object with the TNA object
+          pattern: "tna.rds"
+  - mra_object:
+      - meta:
+          type: file
+          description: TSV file with DEGs names
+          pattern: "*.tsv"
+      - mra.rds:
+          type: file
+          description: TSV file with DEGs names
+          pattern: "*.tsv"
+  - gsea1_object:
+      - meta:
+          type: file
+          description: RDS R Object with the GSEA1 object
+          pattern: "gsea1.rds"
+      - gsea1.rds:
+          type: file
+          description: RDS R Object with the GSEA1 object
+          pattern: "gsea1.rds"
+  - gsea1_plot:
+      - meta:
+          type: file
+          description: PDF file with the GSEA1 plot
+          pattern: "gsea1_plot.pdf"
+      - gsea1_plot.pdf:
+          type: file
+          description: PDF file with the GSEA1 plot
+          pattern: "gsea1_plot.pdf"
+  - gsea2_object:
+      - meta:
+          type: file
+          description: RDS R Object with the GSEA2 object
+          pattern: "gsea2.rds"
+      - gsea2.rds:
+          type: file
+          description: RDS R Object with the GSEA2 object
+          pattern: "gsea2.rds"
+  - gsea2_plot:
+      - meta:
+          type: file
+          description: PDF file with the GSEA2 plot
+          pattern: "gsea2_plot.pdf"
+      - gsea2_plot.pdf:
+          type: file
+          description: PDF file with the GSEA2 plot
+          pattern: "gsea2_plot.pdf"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@mribeirodantas"
+maintainers:
+  - "@mribeirodantas"
diff --git a/modules/nf-core/rtn/tna/templates/rtn_tna.r b/modules/nf-core/rtn/tna/templates/rtn_tna.r
@@ -0,0 +1,113 @@
+#!/usr/bin/env Rscript
+
+# Ported to nf-core/modules with template by Jonathan Manning
+
+#' 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)]
+}
+
+# Load
+library("RTN")
+library("snow")
+
+################################################
+################################################
+## Pull in module inputs                      ##
+################################################
+################################################
+
+tni_object <- readRDS('tni.rds')
+# degs_log2 <- read_tsv
+# degs <- read_tsv
+# degs_annotation <-
+
+output_prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix')
+threads <- $task.cpus
+args_opt <- parse_args('$task.ext.args')
+
+n_perm <- ifelse('n_permutations' %in% names(args_opt), strtoi(args_opt[['n_permutations']]), 10)
+
+# Debug messages (stdout)
+sink(stdout(), type = "message") # sink messages to stdout
+message("Expression matrix file   : ", input_expr_matrix)
+message("Nb permutations          : ", n_perm)
+message("Nb threads               : ", threads)
+message("Output basename          : ", output_prefix)
+if ('tfs' %in% names(args_opt)) {
+    message("TFs                      : ", args_opt[['tfs']])
+    tfs <- strsplit(args_opt[['tfs']], ',')
+} else {
+    # Load data
+    data(tfsData)
+    tfs <- tfsData\$Lambert2018\$SYMBOL
+}
+sink(NULL, type="message") # close the sink
+
+# Input 1: 'object', a TNI object with regulons
+# Input 2: 'phenotype', a named numeric vector, usually log2 differential expression levels
+# Input 3: 'hits', a character vector, usually a set of differentially expressed genes
+# Input 4: 'phenoIDs', an optional data frame with gene anottation mapped to the phenotype
+rtna <- tni2tna.preprocess(object = tni_object, phenotype = degs_log2, hits = degs, phenoIDs = degs_annotation)
+
+# TNA analysis here
+
+saveRDS(rtni, file = "tni.rds")
+saveRDS(rtni_permutation, file = "tni_permutated.rds")
+saveRDS(rtni_bootstrapped, file = "tni_bootstrapped.rds")
+saveRDS(rtni_filtered, file = "tni_filtered.rds")
+
+# Plot
+#pdf(paste0(output_prefix, "_RTN.pdf"))
+#tni.graph(rtni_filtered, regulatoryElements = c("FOXM1", "E2F2"))
+#title("Regulatory Transcriptional Network")
+#mtext(output_prefix, side=3)
+#dev.off
9E81
()
+#cat(
+#    paste("- Threads::", threads),
+#    fill=TRUE, labels=output_prefix,
+#    file=paste0(output_prefix, "_intercept_slope.txt"), append=FALSE
+#)
+
+################################################
+################################################
+## R SESSION INFO                             ##
+################################################
+################################################
+
+sink(paste(output_prefix, "R_sessionInfo.log", sep = '.'))
+print(sessionInfo())
+sink()
+
+################################################
+################################################
+## VERSIONS FILE                              ##
+################################################
+################################################
+
+r.version <- strsplit(version[['version.string']], ' ')[[1]][3]
+rtn.version <- as.character(packageVersion('RTN'))
+
+writeLines(
+    c(
+        '"${task.process}":',
+        paste('    bioconductor-rtn:', rtn.version)
+    ),
+'versions.yml')
+
+################################################
+################################################
+################################################
+################################################
diff --git a/modules/nf-core/rtn/tna/tests/main.nf.test b/modules/nf-core/rtn/tna/tests/main.nf.test
@@ -0,0 +1,70 @@
+nextflow_process {
+
+    name "Test Process RTN_TNA"
+    script "../main.nf"
+    process "RTN_TNA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "rtn"
+    tag "rtn/tni"
+    tag "rtn/tna"
+
+    setup {
+        def content = "CYP24A1\nNNAT\nPHACTR3"
+        def DEGs = file("${workDir}/degs.tsv")
+        DEGs.text = content
+
F438

+        run("RTN_TNI") {
+            script "../../../rtn/tni/main.nf"
+            process {
+                """
+                input[0] = [
+                  [id:'test'],
+                  file(params.modules_testdata_base_path + 'genomics/homo_sapiens/riboseq_expression/salmon.merged.gene_counts_length_scaled.tsv', checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("musmusculus tna expression matrix - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = RTN_TNI.out.tni
+                input[1] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [ file("${workDir}/degs.tsv", checkIfExists: true) ]
+                ])
+                input[2] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/treatment_mCherry_hND6_.deseq2.results_filtered.tsv', checkIfExists: true) ]
+                ])
+                input[3] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [ ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.tna_object[0][1]).exists() },
+                { assert file(process.out.mra_object[0][1]).exists() },
+                { assert file(process.out.gsea1_object[0][1]).exists() },
+                { assert file(process.out.gsea1_plot[0][1]).exists() },
+                { assert file(process.out.gsea2_object[0][1]).exists() },
+                { assert file(process.out.gsea2_plot[0][1]).exists() },
+                { assert file(process.out.versions[0]).exists() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/rtn/tna/tests/nextflow.config b/modules/nf-core/rtn/tna/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: RTN_TNA {
+        ext.args = "--n_permutations 5"
+    }
+}
diff --git a/modules/nf-core/rtn/tna/tests/nextflow.config2 b/modules/nf-core/rtn/tna/tests/nextflow.config2
@@ -0,0 +1,5 @@
+process {
+    withName: RTN_TNA {
+        ext.args = '--tfs ENSG00000125798,ENSG00000125816'
+    }
+}
diff --git a/modules/nf-core/rtn/tna/tests/nextflow.config3 b/modules/nf-core/rtn/tna/tests/nextflow.config3
@@ -0,0 +1,5 @@
+process {
+    withName: RTN_TNA {
+        ext.args = '--n_permutations 12 --tfs ENSG00000125798,ENSG00000125816'
+    }
+}
diff --git a/modules/nf-core/rtn/tna/tests/tags.yml b/modules/nf-core/rtn/tna/tests/tags.yml
@@ -0,0 +1,2 @@
+rtn/tna:
+  - "modules/nf-core/rtn/tna/**"