Contrasts not being processed with DREAM

[grst]

Description of the bug

When running the pipeline with DREAM, VARIANCEPARTITION_DREAM is only executed once, even though there are three contrasts. Even for the one contrast that does get processed, the pipeline does not generate a HTML report, but stops after the CUSTOM_FILTERDIFFERENTIALTABLE process

When inspecting output/tables/differential/BORC_simple_PD_vs_SD_formula_baseline_response_dream.dream.results.tsv (i.e. the UNFILTERED one), it contains only 10 genes, even though the input matrix has ~58k gernes.

Interstingly, when using limma (after which the DREAM modules were modelled), everything works as expected.

Command used and terminal output

nextflow run nf-core/differentialabundance -r 8dc9306 \
    -params-file src/params.yml \
    -profile bi,cluster \
    -c src/nextflow.config \
    -resume

--- 
study_name: "baseline_response_dream"
study_type: "rnaseq"
study_abundance_type: "counts"
input: "../../01_prepare_data/output/rnaseq_baseline/input.tsv"
matrix: "../../01_prepare_data/output/rnaseq_baseline/matrix.tsv"
features: "../../01_prepare_data/output/rnaseq_baseline/features.tsv"
contrasts_yml: "src/contrasts.yml"
outdir: "output"
features_id_col: "gene_id"
features_name_col: "GENESMBL"
shinyngs_build_app: false
filtering_min_samples: 5
filtering_grouping_var: "BORC_simple"
differential_method: "dream"
dream_apply_voom: true
differential_fc_column: "logFC"
differential_pval_column: "P.Value"
differential_qval_column: "adj.P.Val"
differential_feature_id_column: "gene_id"
differential_feature_name_column: "gene_id"
exploratory_assay_names: "raw,normalised"
exploratory_final_assay: "normalised"
exploratory_log2_assays: "raw"


---

contrasts:
  - id: BORC_simple_PD_vs_SD
    comparison: ["BORC_simple", "SD", "PD"]
  - id: BORC_simple_PD_vs_SD_formula
    formula: ~ 0 + BORC_simple
    make_contrasts_str: "BORC_simplePD - BORC_simpleSD"
  - id: BORC_simple_PRCR_vs_SD
    comparison: ["BORC_simple", "SD", "CR/PR"]

Relevant files

No response

System information

No response