From db4e959690dda4243f1ec56d15550dd1c2ebf55a Mon Sep 17 00:00:00 2001 From: Kamil Malisz Date: Wed, 3 Jul 2024 13:54:59 +0200 Subject: [PATCH] Lima integration wip --- modules/nf-core/limma/differential/main.nf | 8 +++++++- .../templates/{limma_de.R => limma_de_micro_array.R} | 0 nextflow_schema.json | 2 +- workflows/differentialabundance.nf | 3 ++- 4 files changed, 10 insertions(+), 3 deletions(-) rename modules/nf-core/limma/differential/templates/{limma_de.R => limma_de_micro_array.R} (100%) diff --git a/modules/nf-core/limma/differential/main.nf b/modules/nf-core/limma/differential/main.nf index 384e4649..f13db84f 100644 --- a/modules/nf-core/limma/differential/main.nf +++ b/modules/nf-core/limma/differential/main.nf @@ -10,6 +10,7 @@ process LIMMA_DIFFERENTIAL { input: tuple val(meta), val(contrast_variable), val(reference), val(target) tuple val(meta2), path(samplesheet), path(intensities) + val type output: tuple val(meta), path("*.limma.results.tsv") , emit: results @@ -23,5 +24,10 @@ process LIMMA_DIFFERENTIAL { task.ext.when == null || task.ext.when script: - template 'limma_de.R' + if (type == 'rnaseq') { + template 'limma_de_rna_seq.R' + } else { + template 'limma_de_micro_array.R' + } + } diff --git a/modules/nf-core/limma/differential/templates/limma_de.R b/modules/nf-core/limma/differential/templates/limma_de_micro_array.R similarity index 100% rename from modules/nf-core/limma/differential/templates/limma_de.R rename to modules/nf-core/limma/differential/templates/limma_de_micro_array.R diff --git a/nextflow_schema.json b/nextflow_schema.json index 831a9295..30a54cb1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1314,7 +1314,7 @@ "$ref": "#/definitions/deseq2_specific_options_rna_seq_only" }, { - "$ref": "#/definitions/limma_specific_options_microarray_only" + "$ref": "#/definitions/limma_specific_options" }, { "$ref": "#/definitions/gsea" diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf index 67f428d2..f6e281f9 100644 --- a/workflows/differentialabundance.nf +++ b/workflows/differentialabundance.nf @@ -346,7 +346,8 @@ workflow DIFFERENTIALABUNDANCE { LIMMA_DIFFERENTIAL ( ch_contrasts, - ch_samples_and_matrix + ch_samples_and_matrix, + params.study_type ) ch_differential = LIMMA_DIFFERENTIAL.out.results ch_model = LIMMA_DIFFERENTIAL.out.model