From e1c52e15b14bb51a003ae13579a1e99d6bad197c Mon Sep 17 00:00:00 2001 From: Ido Tamir Date: Fri, 18 Oct 2024 13:34:27 +0200 Subject: [PATCH 1/2] allow integer sample names Validation of file failed: -> Entry 1: Error for field 'sample' (298098): Sample name must be provided and cannot contain spaces --- assets/schema_input.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 980a829ea..dc330e9cd 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -8,7 +8,7 @@ "type": "object", "properties": { "sample": { - "type": "string", + "type": ["string", "integer"], "pattern": "^\\S+$", "errorMessage": "Sample name must be provided and cannot contain spaces", "meta": ["id"] From 7d3daa4d290cbc66fc4048a2ea315393223bfaae Mon Sep 17 00:00:00 2001 From: Ido Tamir Date: Tue, 17 Jun 2025 16:26:44 +0200 Subject: [PATCH 2/2] umi dedup fix for mqc --- workflows/rnaseq/assets/multiqc/multiqc_config.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index a60c89347..908ef5cca 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -210,6 +210,11 @@ sp: picard/wgs_metrics: skip: true + + +fn_ignore_files: + - "*umi_dedup.transcriptome.sorted.log" + # See https://github.com/ewels/MultiQC_TestData/blob/master/data/custom_content/with_config/table_headerconfig/multiqc_config.yaml custom_data: fail_trimmed_samples: