From 4477e1c88ccbd216e62d435ab6e157ecb14d380f Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Tue, 29 Oct 2024 11:48:29 +0100 Subject: [PATCH] add limma to test_experimental --- assets/tools_samplesheet.csv | 2 +- conf/test_experimental.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/tools_samplesheet.csv b/assets/tools_samplesheet.csv index 2289918d..c0e1c1c8 100644 --- a/assets/tools_samplesheet.csv +++ b/assets/tools_samplesheet.csv @@ -6,7 +6,7 @@ propd_ora,propd,,,,gprofiler2, deseq2_gsea,deseq2,,,,gsea, deseq2_ora,deseq2,,,,gprofiler2, limma,limma,,,,, -limma_gsea,limma,,,,gsea, +limma_ora,limma,,,,gprofiler2, pcorbshrink,,,propr,--metric pcor.bshrink,, propr,,,propr,--metric rho,, cor,,,propr,--metric cor,, diff --git a/conf/test_experimental.config b/conf/test_experimental.config index 88506222..0fdeff51 100644 --- a/conf/test_experimental.config +++ b/conf/test_experimental.config @@ -29,7 +29,7 @@ params { input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv' matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv' contrasts = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv' - pathway = "propd,propr,cor,propd_grea" + pathway = "propd,propd_grea,limma,propr,cor" // some pathways are not included in the test, because they don't make sense to test for this dataset // for example propd_fdr don't give significant results on this dataset, and the permutation will be scaped