From 0dd0c3673a98231292c1b8abb28c49a039b8dcfb Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Tue, 13 Aug 2024 10:21:11 +0200 Subject: [PATCH] fix: make the `aux-files` example use the existing `ANN` field `SYMBOL` (#320) * fix: make the `aux-files` example use the existing `ANN` field `SYMBOL` This has tripped up multiple people by now, so let's fix the example in the standard `config/config.yaml` that everybody gets upon module-based deployment. * fix: also update .test/config-no-candidate-filtering/config.yaml --- .test/config-no-candidate-filtering/config.yaml | 2 +- config/config.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.test/config-no-candidate-filtering/config.yaml b/.test/config-no-candidate-filtering/config.yaml index a5f6752b..54cae9d4 100644 --- a/.test/config-no-candidate-filtering/config.yaml +++ b/.test/config-no-candidate-filtering/config.yaml @@ -48,7 +48,7 @@ calling: with_aux: aux-files: super_interesting_genes: config-no-candidate-filtering/super_interesting_genes.tsv - expression: "ANN['GENE'] in AUX['super_interesting_genes']" + expression: "ANN['SYMBOL'] in AUX['super_interesting_genes']" fdr-control: threshold: 0.05 events: diff --git a/config/config.yaml b/config/config.yaml index 20456024..29638874 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -119,7 +119,7 @@ calling: gene_list_filter: aux-files: super_interesting_genes: "config/super_interesting_genes.tsv" - expression: "ANN['GENE'] in AUX['super_interesting_genes']" + expression: "ANN['SYMBOL'] in AUX['super_interesting_genes']" fdr-control: threshold: 0.05 # denote FDR control mode, see https://varlociraptor.github.io/docs/filtering