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‎CHANGELOG.md‎

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@@ -39,7 +39,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Changed
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- [[#468](https://github.com/nf-core/differentialabundance/pull/468)] - Template update for nf-core/tools v3.3.1.
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- [[#468](https://github.com/nf-core/differentialabundance/pull/468)] - Template update for nf-core/tools v3.3.1 ([@SusiJo](https://github.com/SusiJo), reviewed by [@famosab](https://github.com/famosab), [@mashehu](https://github.com/mashehu))
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- [[#448](https://github.com/nf-core/differentialabundance/pull/448)] - Simplify toolsheet handling and restructure workflow to use paramset in meta. ([@pinin4fjords](https://github.com/pinin4fjords), review by [@suzannejin](https://github.com/suzannejin) and [@grst](https://github.com/grst))
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- [[#431](https://github.com/nf-core/differentialabundance/pull/431)] - Replace the calls to differential and functional analysis modules by subworkflows. ([@suzannejin](https://github.com/suzannejin), review by [@pinin4fjords](https://github.com/pinin4fjords))
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- [[#410](https://github.com/nf-core/differentialabundance/pull/410)] - Update contrasts file format to allow yaml ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords)).

‎nf-test.config‎

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configFile "tests/nextflow.config"
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// ignore tests coming from the nf-core/modules repo
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ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*'
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ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'
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// run all test with defined profile(s) from the main nextflow.config
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profile "test"

‎tests/default.nf.test‎

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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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}
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}
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when {
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params {
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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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‎tests/nextflow.config‎

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params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
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params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance'
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aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
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// fixes S3 access issues on self-hosted runners
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aws.client.anonymous = true
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process {

‎tests/test_affy.nf.test‎

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params {
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outdir = "$outputDir"
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study_name = 'GSE50790'
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}
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}
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‎tests/test_custom_paramsheet.nf.test‎

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paramsheet = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/test_custom_paramsheet.csv"
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paramset_name = "deseq2"
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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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gtf = 'https://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz'
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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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}
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}
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paramsheet = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/test_custom_paramsheet.csv"
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paramset_name = "gsea"
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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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gtf = 'https://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz'
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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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}
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}
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paramsheet = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/test_custom_paramsheet.csv"
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paramset_name = "gprofiler2"
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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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gtf = 'https://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz'
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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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}
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}
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‎tests/test_maxquant.nf.test‎

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study_name = 'PXD043349'
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config_profile_name = 'MaxQuant test profile'
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config_profile_description = 'MaxQuant test dataset to check pipeline function'
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}
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}
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}
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then {

‎tests/test_nogtf.nf.test‎

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when {
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outdir = "$outputDir"
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outdir = "$outputDir"
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}
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}
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then {

‎tests/test_rnaseq_dream.nf.test‎

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paramset_name = "dream_rnaseq"
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differential_method = null
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functional_method = null
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}
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}
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}
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test("Test rnaseq dream profile - complex contrast") {
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when {
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params {
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outdir = "$outputDir"
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}
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}
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‎tests/test_rnaseq_limma.nf.test‎

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when {
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params {
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outdir = "$outputDir"
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}
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}
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