Tetranscripts

modules/nf-core/tetranscripts/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::tetranscripts=2.2.3"

modules/nf-core/tetranscripts/main.nf

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+process TETRANSCRIPTS {
+    tag "$meta_c.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/tetranscripts:2.2.3--pyh7cba7a3_0':
+        'biocontainers/tetranscripts:2.2.3--pyh7cba7a3_0' }"
+
+    input:
+    tuple val(meta_t), path(bam_t)
+    tuple val(meta_c), path(bam_c)
+    tuple val(meta_ggtf), path(g_gtf)
+    tuple val(meta_tegtf), path(te_gtf)
+
+    output:
+    tuple val(meta_t), path("*.cntTable"), emit: countTable
+    tuple val(meta_t), path("*.R"), emit: log2fc
+    tuple val(meta_t), path("*_analysis.txt"), emit: analysis, optional: true
+    tuple val(meta_t), path("*_gene_TE.txt"), emit: sigdiff, optional: true
+    tuple val("${task.process}"), val('tetranscripts'), eval("tetranscripts version | sed '1!d;s/.* //'"), emit: versions_tetranscripts, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta_c.id}"
+// Join multiple BAM files with spaces for -t and -c arguments
+    def treatment_bams = [bam_t].flatten().join(' ')
+    def control_bams = [bam_c].flatten().join(' ')
+    """
+    TEtranscripts \\
+	-t ${treatment_bams} \\
+	-c ${control_bams} \\
+	--GTF $g_gtf \\
+	--TE $te_gtf \\
+	--project ${prefix} \\
+        $args
+
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta_c.id}"
+    """
+    echo $args
+
+    touch ${prefix}.R
+    touch ${prefix}.cntTable
+    touch ${prefix}_gene_TE_analysis.txt
+    touch ${prefix}_sigdiff_gene_TE.txt
+
+    """
+}

modules/nf-core/tetranscripts/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "tetranscripts"
+description: Runs TEtranscripts which summarises transposable element content of
+  a bam file.
+keywords:
+  - transposable
+  - TE
+  - transcriptomics
+tools:
+  - "tetranscripts":
+      description: A package for including transposable elements in differential
+        enrichment analysis of sequencing datasets.
+      homepage: https://github.com/mhammell-laboratory/TEtranscripts
+      documentation: https://hammelllab.labsites.cshl.edu/software/#TEtranscripts
+      tool_dev_url: https://github.com/mhammell-laboratory/TEtranscripts
+      doi: 10.1093/bioinformatics/btv422
+      licence: ["GPL v3"]
+      identifier: biotools:tetranscripts
+
+input:
+  # Treatment BAM
+  - - meta_t:
+        type: map
+        description: |
+          Groovy Map containing treatment sample information. e.g. `[
+          id:'sample1' ]`
+    - bam_t:
+        type: file
+        description: A BAM file for the treatment condition
+        pattern: "*.{bam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572"
+
+        # Control BAM
+  - - meta_c:
+        type: map
+        description: |
+          Groovy Map containing control sample information,
+          e.g. `[ id:'control1']`
+    - bam_c:
+        type: file
+        description: A BAM file for the control condition
+        pattern: "*.{bam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572"
+
+        # Genome GTF
+  - - meta_ggtf:
+        type: map
+        description: |
+          Groovy map containing control sample information
+          e.g. `[ id:'control1' ]`
+    - g_gtf:
+        type: file
+        description: A GTF file for alignment to the genome
+        pattern: "*.{gtf}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2306"
+
+        # TE GTF
+  - - meta_tegtf:
+        type: map
+        description: |
+          Groovy map containing TE GTF information
+          e.g. `[ id:'control1' ]`
+
+    - te_gtf:
+        type: file
+        description: A curated GTF file for alignment to transposable elements
+        pattern: "*.{gtf}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2306"
+output:
+  countTable:
+    - - meta_t:
+          type: map
+          description: |
+            Groovy Map containing treatment sample information.
+            e.g. `id:'sample1' ]`
+      - "*.cntTable":
+          type: file
+          description: Counts table of transposable element families
+          pattern: "*.cntTable"
+          ontologies: []
+  log2fc:
+    - - meta_t:
+          type: map
+          description: |
+            Groovy Map containing treatment sample information.
+            e.g. `id:'sample1' ]`
+      - "*.R":
+          type: file
+          description: Differential gene expression analysis file
+          pattern: "*.R"
+
+          ontologies:
+            - edam: http://edamontology.org/format_3999 # R script
+
+  analysis:
+    - - meta_t:
+          type: map
+          description: |
+            Groovy map containing treatment sample information.
+            e.g. `id:'sample1' ]`
+      - "*_analysis.txt":
+          type: file
+          description: DESeq2 analysis file
+          pattern: "*_analysis.txt"
+          ontologies:
+            - edam: http://edamontology.org/format_2330 # text format
+
+  sigdiff:
+    - - meta_t:
+          type: map
+          description: |
+            Groovy map containing treatment sample information.
+            e.g. `id:'sample1' ]`
+      - "*_gene_TE.txt":
+          type: file
+          description: DESeq2 analysis file
+          pattern: "*_gene_TE.txt"
+          ontologies:
+            - edam: http://edamontology.org/format_2330 # text format
+
+  versions_tetranscripts:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - tetranscripts:
+          type: string
+          description: The tool name
+      - "tetranscripts version | sed '1!d;s/.* //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - tetranscripts:
+          type: string
+          description: The tool name
+      - "tetranscripts version | sed '1!d;s/.* //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@hanalysis"
+maintainers:
+  - "@hanalysis"

modules/nf-core/tetranscripts/tests/main.nf.test

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+// nf-core modules test tetranscripts
+nextflow_process {
+
+    name "Test Process TETRANSCRIPTS"
+    script "../main.nf"
+    process "TETRANSCRIPTS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tetranscripts"
+
+    test("single file c and t - bam") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'ctrl_bam' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    [],
+                ]
+
+		input[1] = [
+                    [ id:'test_bam' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true),
+                    [],
+                ]
+		input[2] = [
+                    [ id:'genome_gtf' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true),
+                ]
+		input[3] = [
+                    [ id:'te_gtf' ],
+                    file('https://raw.githubusercontent.com/hanalysis/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/chr21/sequence/GRCh38_GENCODE_rmsk_TE_chr21.gtf', checkIfExists: true),
+                ]
+                """
+
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("multiple files t - bam") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'ctrl_bam' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    [],
+                ]
+
+                input[1] = [
+                    [ id:'test_bam' ],
+                   [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam', checkIfExists: true),],
+                    []
+                ]
+                input[2] = [
+                    [ id:'genome_gtf' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true),
+                ]
+                input[3] = [
+                    [ id:'te_gtf' ],
+                    file('https://raw.githubusercontent.com/hanalysis/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/chr21/sequence/GRCh38_GENCODE_rmsk_TE_chr21.gtf', checkIfExists: true),
+                ]
+                """
+
+            }
+        }
+
+        then {
+            assert process.success
+
+            def outputFile = path(process.out.countTable[0][1]) // [0] is first sample, [1] is file (not meta)
+            assert outputFile.exists()
+
+            def lines = outputFile.readLines()
+            // take first 5 lines to check
+            def firstLines = lines.take(5)
+
+            // Check 4 columns (row names + 3 samples)
+            firstLines.eachWithIndex { line, idx ->
+               def columns = line.split(/\s+/)
+               assert columns.size() == 4: "Line ${idx + 1}: Expected 4 columns but got ${columns.size()} in line: '${line}'"
+            }
+
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("single file c and t - bam - stub") {
+
+        options "-stub"
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+		input[0] = [
+                    [ id:'ctrl_bam' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    [],
+                ]
+
+                input[1] = [
+                    [ id:'test_bam' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true),
+                    [],
+                ]
+                input[2] = [
+                    [ id:'genome_gtf' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true),
+                ]
+                input[3] = [
+                    [ id:'te_gtf' ],
+                    file('https://raw.githubusercontent.com/hanalysis/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/chr21/sequence/GRCh38_GENCODE_rmsk_TE_chr21.gtf', checkIfExists: true),
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+}