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SusiJoSusiJo
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update tests
1 parent 6e45682 commit 9fa6a00

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Lines changed: 1181 additions & 95 deletions

‎tests/default.nf.test‎

Lines changed: 198 additions & 6 deletions
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nextflow_pipeline {
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name "Test pipeline"
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name "Test Workflow main.nf - DIFFERENTIALABUNDANCE (test)"
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script "../main.nf"
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tag "test"
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tag "pipeline"
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config "../conf/rnaseq.config"
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profile "test"
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test("-profile test") {
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test("Test profile - with toolsheet") {
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when {
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params {
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outdir = "$outputDir"
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outdir = "$outputDir"
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paramset_name = "deseq2_rnaseq_gsea"
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differential_method = null
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functional_method = null
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study_name = 'SRP254919'
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config_profile_name = 'Test profile'
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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/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv'
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matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv'
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transcript_length_matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.spoofed_lengths.tsv'
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contrasts_yml = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/SRP254919.contrasts.yaml'
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// To do: replace this with a cut-down mouse GTF matching the matrix for testing
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gtf = 'https://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz'
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// Observations
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observations_id_col = 'sample'
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observations_name_col = 'sample'
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// Apply a higher filter to check that the filtering works
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filtering_min_abundance = 10
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// Exploratory
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exploratory_main_variable = 'contrasts'
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// Test dataset is too small for the nsub default value
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deseq2_vst_nsub = 500
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// IMMUNEDECONV
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immunedeconv_run = true
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immunedeconv_method = "mmcp_counter"
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immunedeconv_function = "deconvolute_mouse"
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// Activate GSEA
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functional_method = 'gsea'
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gene_sets_files = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt'
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gsea_rnd_seed = '10'
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// Report options
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report_contributors = 'Jane Doe\nDirector of Institute of Microbiology\nUniversity of Smallville;John Smith\nPhD student\nInstitute of Microbiology\nUniversity of Smallville'
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// Other
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round_digits = 3
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}
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}
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then {
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// stable_name: All files + folders in ${params.outdir}/ with a stable name
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def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
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// stable_path: All files in ${params.outdir}/ with stable content
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def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
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assertAll(
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{ assert workflow.success},
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{ assert snapshot(
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents
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stable_path
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).match() }
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)
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}
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}
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test("Test profile - csv contrasts") { // make sure we keep backwards compatibility with csv contrasts
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when {
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params {
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study_name = 'SRP254919'
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config_profile_name = 'Test profile'
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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/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv'
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matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv'
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transcript_length_matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.spoofed_lengths.tsv'
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contrasts_yml = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/SRP254919.contrasts.yaml'
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// To do: replace this with a cut-down mouse GTF matching the matrix for testing
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gtf = 'https://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz'
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// Observations
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observations_id_col = 'sample'
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observations_name_col = 'sample'
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// Apply a higher filter to check that the filtering works
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filtering_min_abundance = 10
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// Exploratory
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exploratory_main_variable = 'contrasts'
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// Test dataset is too small for the nsub default value
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deseq2_vst_nsub = 500
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// IMMUNEDECONV
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immunedeconv_run = true
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immunedeconv_method = "mmcp_counter"
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immunedeconv_function = "deconvolute_mouse"
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// Activate GSEA
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functional_method = 'gsea'
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gene_sets_files = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt'
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gsea_rnd_seed = '10'
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// Report options
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report_contributors = 'Jane Doe\nDirector of Institute of Microbiology\nUniversity of Smallville;John Smith\nPhD student\nInstitute of Microbiology\nUniversity of Smallville'
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// Other
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round_digits = 3
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outdir = "$outputDir"
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contrasts_yml = null
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contrasts = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv"
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}
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}
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then {
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// stable_name: All files + folders in ${params.outdir}/ with a stable name
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def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
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// stable_path: All files in ${params.outdir}/ with stable content
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def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
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assertAll(
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{ assert workflow.success},
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{ assert snapshot(
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents
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stable_path
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).match() }
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)
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}
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}
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test("Test profile - yml no formula") { // make sure we keep backwards compatibility with yaml contrasts that don't use formula
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when {
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params {
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study_name = 'SRP254919'
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config_profile_name = 'Test profile'
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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/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv'
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matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv'
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transcript_length_matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.spoofed_lengths.tsv'
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contrasts_yml = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/SRP254919.contrasts.yaml'
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// To do: replace this with a cut-down mouse GTF matching the matrix for testing
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gtf = 'https://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz'
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// Observations
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observations_id_col = 'sample'
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observations_name_col = 'sample'
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// Apply a higher filter to check that the filtering works
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filtering_min_abundance = 10
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// Exploratory
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exploratory_main_variable = 'contrasts'
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// Test dataset is too small for the nsub default value
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deseq2_vst_nsub = 500
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// IMMUNEDECONV
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immunedeconv_run = true
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immunedeconv_method = "mmcp_counter"
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immunedeconv_function = "deconvolute_mouse"
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// Activate GSEA
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functional_method = 'gsea'
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gene_sets_files = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt'
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gsea_rnd_seed = '10'
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// Report options
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report_contributors = 'Jane Doe\nDirector of Institute of Microbiology\nUniversity of Smallville;John Smith\nPhD student\nInstitute of Microbiology\nUniversity of Smallville'
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outdir = "$outputDir"
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}
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}
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@@ -22,14 +214,14 @@ nextflow_pipeline {
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{ assert snapshot(
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_mqc_versions.yml"),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents
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stable_path
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).match() }
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)
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)
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}
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}
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}

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