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Merge pull request #446 from atrigila/add_variancepartition_dream
Add `variancepartition/dream`
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‎CHANGELOG.md‎

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### Added
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- [[#441](https://github.com/nf-core/differentialabundance/pull/441)] - Add dream differential module. ([@nschcolnicov](https://github.com/nschcolnicov) and [@alanmmobbs93](https://github.com/alanmobbs93), review by [@pinin4fjords](https://github.com/pinin4fjords), [@suzannejin](https://github.com/suzannejin) and [@grst](https://github.com/grst)).
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- [[#440](https://github.com/nf-core/differentialabundance/pull/440)] - Add handling for formula based contrasts. ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords))
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- [[#437](https://github.com/nf-core/differentialabundance/pull/437)] - Add nf-tests to deseq2/differential, rmarkdownnotebook, and proteus modules. ([@nschcolnicov](https://github.com/nschcolnicov), review by [@TODO](TODO)).
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- [[#431](https://github.com/nf-core/differentialabundance/pull/431)] - Add differential and functional subworkflows. ([@suzannejin](https://github.com/suzannejin), co-authored by [@bjlang](https://github.com/bjlang) and [@caraiz2001](https://github.com/caraiz2001), review by [@pinin4fjords](https://github.com/pinin4fjords))

‎conf/modules.config‎

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].join(' ').trim() }
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}
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withName: VARIANCEPARTITION_DREAM {
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publishDir = [
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[
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path: { "${params.outdir}/tables/differential" },
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mode: params.publish_dir_mode,
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pattern: '*.dream.results.tsv'
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]
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]
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}
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withName: CUSTOM_FILTERDIFFERENTIALTABLE {
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ext.prefix = { "${input_file.toString().split("\\.").init().join(".")}" }
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publishDir = [

‎conf/rnaseq_dream.config‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running RNA-seq analysis
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines settings specific to RNA-seq analysis
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Use as follows:
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nextflow run nf-core/differentialabundance -profile rnaseq_dream,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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params {
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config_profile_name = 'RNA-seq profile with `VARIANCEPARTITION_DREAM`'
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config_profile_description = 'Settings for RNA-seq analysis with `VARIANCEPARTITION_DREAM`'
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// Study
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study_type = 'rnaseq'
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study_abundance_type = 'counts'
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// Observations
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observations_id_col = 'sampleId'
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observations_name_col = 'sampleId'
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// Differential options
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differential_use_dream = true
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differential_file_suffix = ".dream.results.tsv"
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differential_fc_column = "logFC"
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differential_pval_column = "P.Value"
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differential_qval_column = "adj.P.Val"
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differential_feature_id_column = "Geneid"
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differential_feature_name_column = "Geneid"
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}

‎conf/test_rnaseq_dream.config‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running RNA-seq analysis
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines settings specific to RNA-seq analysis
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Use as follows:
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nextflow run nf-core/differentialabundance -profile test_rnaseq_dream,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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includeConfig 'rnaseq_dream.config'
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params {
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study_name = 'SRP254919'
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config_profile_name = 'Test RNAseq with DREAM'
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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/formula_contrasts/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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// Features
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features_type = 'gene'
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features_id_col = 'gene_id'
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features_name_col = 'gene_name'
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features_metadata_cols = 'gene_id,gene_name,gene_biotype'
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// Differential options
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differential_feature_id_column = "gene_id"
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differential_feature_name_column = "gene_name"
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differential_fc_column = "logFC"
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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_assay_names = "raw,normalised"
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exploratory_final_assay = "normalised"
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exploratory_log2_assays = 'raw,normalised'
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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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// Activate GSEA
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gsea_run = true
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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_round_digits = 3
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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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}
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‎docs/output.md‎

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- `raw.matrix.tsv`: RMA background corrected matrix (Affy)
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- `normalised.matrix.tsv`: RMA background corrected and normalised intensities matrix (Affy)
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- `differential/`: Directory containing tables of differential statistics reported by differential modules such as DESeq2
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- `[contrast_name].[deseq2|limma].results.tsv`: Results of DESeq2 differential analyis (RNA-seq) OR Limma differential analysis (Affymetrix arrays, GEO studies, Maxquant proteomics studies)
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- `[contrast_name].[deseq2|dream|limma].results.tsv`: Results of DESeq2 differential analyis (RNA-seq), DREAM differential analysis (RNA-seq for mixed linear models) OR Limma differential analysis (Affymetrix arrays, GEO studies, Maxquant proteomics studies)
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- `[contrast_name].[deseq2|limma].results_filtered.tsv`: Results of DESeq2 differential analyis (RNA-seq) OR Limma differential analysis (Affymetrix arrays, GEO studies, Maxquant proteomics studies); filtered for differentially abundant entries
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- `immunedeconv/`: Directory containing table of immunedeconv results
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- `${prefix}.deconvolution_results.tsv`: TSV output that contains estimated proportions of immune cell types for each sample

‎modules.json‎

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},
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"deseq2/differential": {
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"branch": "master",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"git_sha": "25c228dd132d91596e87b636b0e03fd48d4c951a",
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"installed_by": ["abundance_differential_filter"]
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},
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"geoquery/getgeo": {
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},
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"limma/differential": {
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"branch": "master",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"git_sha": "25c228dd132d91596e87b636b0e03fd48d4c951a",
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"installed_by": ["abundance_differential_filter"]
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},
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"propr/grea": {
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"branch": "master",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["differential_functional_enrichment"]
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},
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"propr/propd": {
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"branch": "master",
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"git_sha": "785efc640b1e87e9ff4b451cf9b6970f0db7a03b",
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"git_sha": "25c228dd132d91596e87b636b0e03fd48d4c951a",
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"installed_by": ["abundance_differential_filter"]
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},
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"proteus/readproteingroups": {
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},
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"shinyngs/validatefomcomponents": {
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"branch": "master",
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"git_sha": "597771ff67e7d86a0ded1561eaa791b19c55deaa",
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"git_sha": "0d290ba0c91d488a47726adedc176f5fe443cf19",
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"installed_by": ["modules"]
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},
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"untar": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"installed_by": ["modules"]
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},
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"variancepartition/dream": {
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"branch": "master",
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"git_sha": "25c228dd132d91596e87b636b0e03fd48d4c951a",
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"installed_by": ["abundance_differential_filter", "modules"]
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},
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"zip": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"nf-core": {
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"abundance_differential_filter": {
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"branch": "master",
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"git_sha": "69b763e449ed23cb0faf2805b4b479f69c168782",
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"git_sha": "25c228dd132d91596e87b636b0e03fd48d4c951a",
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"installed_by": ["subworkflows"]
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},
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"differential_functional_enrichment": {
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"branch": "master",
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"git_sha": "100b1dc1ece11cf8d4fec100314d616a66a60875",
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"git_sha": "25c228dd132d91596e87b636b0e03fd48d4c951a",
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"installed_by": ["subworkflows"]
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},
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"utils_nextflow_pipeline": {

‎modules/nf-core/deseq2/differential/main.nf‎

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