From f63d810e4ef8536f9e15cd648e337e27661f12e2 Mon Sep 17 00:00:00 2001 From: jemten Date: Wed, 14 Aug 2024 11:14:53 +0200 Subject: [PATCH] makes 0 an allowed value for sex --- CHANGELOG.md | 1 + assets/schema_input.json | 2 +- docs/usage.md | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2c4667bd..35d0b5f5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Allow `0` as a valid value for `sex` in the samplesheet [#595](https://github.com/nf-core/raredisease/pull/587) - Updated deepvariant to version 1.6.1 [#587](https://github.com/nf-core/raredisease/pull/587) - Parallelized vcfanno [#585](https://github.com/nf-core/raredisease/pull/585) - Skip ROH calling with bcftools if there are no affected samples [#579](https://github.com/nf-core/raredisease/pull/579) diff --git a/assets/schema_input.json b/assets/schema_input.json index 38249daa..3dddc6a4 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -42,7 +42,7 @@ "sex": { "type": "string", "meta": ["sex"], - "enum": ["1", "2", "other"], + "enum": ["1", "2", "0", "other"], "errorMessage": "Sex must be provided and cannot contain spaces" }, "phenotype": { diff --git a/docs/usage.md b/docs/usage.md index 66d0b357..f3c2bf0f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -108,7 +108,7 @@ nf-core/raredisease will auto-detect whether a sample is single- or paired-end u | `lane` | Used to generate separate channels during the alignment step. | | `fastq_1` | Absolute path to FASTQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | | `fastq_2` | Absolute path to FASTQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `sex` | Sex (1=male; 2=female; other=unknown). | +| `sex` | Sex (1=male; 2=female; for unknown sex use 0 or other). | | `phenotype` | Affected status of patient (0 = missing; 1=unaffected; 2=affected). | | `paternal_id` | Sample ID of the father, can be blank if the father isn't part of the analysis or for samples other than the proband. | | `maternal_id` | Sample ID of the mother, can be blank if the mother isn't part of the analysis or for samples other than the proband. |