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nschcolnicovnschcolnicov
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Added compute_gene_scores nftest and standardized format of module
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‎CHANGELOG.md‎

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@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### `Added`
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- [#94](https://github.com/nf-core/nanostring/pull/94) - Added nf-tests for local subworkflows normalize and quality_control.
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- [#101](https://github.com/nf-core/nanostring/pull/101) - Added nf-test for local module compute_gene_scores.
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### `Fixed`
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‎conf/test_scores.config‎

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@@ -24,7 +24,7 @@ params {
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config_profile_description = 'Minimal test dataset to check pipeline function'
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// Input data
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/samplesheets/samplesheet_test.csv'
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gene_score_yaml = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/gene_score_test.yaml'
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/samplesheets/samplesheet_test.csv'
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gene_score_yaml = params.pipelines_testdata_base_path + 'nanostring/gene_score_test.yaml'
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}

‎modules/local/compute_gene_scores/environment.yml‎

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name: compute_gene_scores
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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- bioconda::multiqc=1.24.1
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- conda-forge::r-yaml=2.3.7
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- conda-forge::r-ggplot2=3.4.4
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- conda-forge::r-dplyr=1.1.4
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- conda-forge::r-stringr=1.5.0
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- bioconda::bioconductor-gsva=1.46.0
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- bioconda::bioconductor-singscore=1.18.0
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- conda-forge::r-factominer=2.8.0
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- conda-forge::r-tibble=3.2.1
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- conda-forge::r-matrixstats=1.1.0

modules/local/compute_gene_scores.nf renamed to modules/local/compute_gene_scores/main.nf

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process COMPUTE_GENE_SCORES {
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label 'process_single'
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conda "r-yaml=2.3.7 r-ggplot2=3.4.4 r-dplyr=1.1.4 r-stringr=1.5.0 bioconductor-gsva=1.46.0 bioconductor-singscore=1.18.0 r-factominer=2.8.0 r-tibble=3.2.1 r-matrixstats=1.1.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-e6920e60d80922852a1b19630ebe16754cf5320d:75e2c0a29159bae8a964e43ae16a45c282fdf651-0' :
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'biocontainers/mulled-v2-e6920e60d80922852a1b19630ebe16754cf5320d:75e2c0a29159bae8a964e43ae16a45c282fdf651-0' }"
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path geneset_yaml
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output:
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path "*.txt", emit: scores_for_mqc
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path "versions.yml" , emit: versions
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path "*.txt" , emit: scores_for_mqc
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when

‎modules/local/compute_gene_scores/meta.yml‎

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name: compute_gene_scores
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description: calculate gene set enrichment scores using multiple methods.
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keywords:
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- bioinformatics tools
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tools:
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- compute_gene_scores:
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description: |
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Compute gene scores calculates gene set scores using various methods such as Singscore, GSVA, SSGSEA, PLAGE, and Samsscore.
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It includes multiple gene set transformations and scoring techniques.
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input:
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- - counts:
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type: file
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description: |
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A matrix or data frame containing normalized gene counts data.
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pattern: "*normalized_counts.tsv"
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- - geneset_yaml:
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type: file
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description: |
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This sets the YAML to be used for computing the gene scores. Needs both a name for each set of genes and respective genes to be selected.
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output:
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- scores_for_mqc:
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- "*.txt":
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type: file
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description: |
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A file containing the calculated scores to be used to create the MultiQC report.
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pattern: "*.txt"
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- versions:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@apeltzer"
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- "@christopher-mohr"
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maintainers:
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- "@nschcolnicov"

‎modules/local/compute_gene_scores/tests/main.nf.test‎

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nextflow_process {
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name "Test Process COMPUTE_GENE_SCORES"
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script "../main.nf"
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process "COMPUTE_GENE_SCORES"
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tag "modules"
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tag "modules_nfcore"
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tag "compute_gene_scores"
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test("test profile") {
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setup {
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run("NACHO_NORMALIZE") {
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script "../../nacho/normalize.nf"
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process {
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"""
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input[0] = Channel.of(
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[
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file(params.pipelines_testdata_base_path + 'nanostring/RCC_files/salmon_01_01.RCC', checkIfExists: true),
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file(params.pipelines_testdata_base_path + 'nanostring/RCC_files/salmon_02_02.RCC', checkIfExists: true),
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file(params.pipelines_testdata_base_path + 'nanostring/RCC_files/salmon_03_03.RCC', checkIfExists: true),
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file(params.pipelines_testdata_base_path + 'nanostring/RCC_files/salmon_04_04.RCC', checkIfExists: true)
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]
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)
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input[1] = file(params.pipelines_testdata_base_path + 'nanostring/samplesheets/samplesheet_test.csv', checkIfExists: true)
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"""
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}
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}
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}
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when {
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process {
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"""
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input[0] = NACHO_NORMALIZE.out.normalized_counts
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input[1] = file(params.pipelines_testdata_base_path + 'nanostring/gene_score_test.yaml', checkIfExists: true )
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() },
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)
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}
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}
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}

‎modules/local/compute_gene_scores/tests/main.nf.test.snap‎

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{
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"test profile": {
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"content": [
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{
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"0": [
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[
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"signature_scores_mqc.txt:md5,315dc730c79b02067b542074eaeb07b9",
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"signature_scores_qc_mqc.txt:md5,88ec48e1d7488357663557b378615923"
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]
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],
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"1": [
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"versions.yml:md5,61fc461ef40beb8b95aa31c8ee4d6760"
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],
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"scores_for_mqc": [
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[
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"signature_scores_mqc.txt:md5,315dc730c79b02067b542074eaeb07b9",
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"signature_scores_qc_mqc.txt:md5,88ec48e1d7488357663557b378615923"
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]
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],
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"versions": [
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"versions.yml:md5,61fc461ef40beb8b95aa31c8ee4d6760"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.10.1"
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},
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"timestamp": "2024-11-19T18:06:40.93622974"
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}
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}

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