Merge branch 'dev' into update-docs

nf-core · Aug 14, 2024 · 01a7b42 · 01a7b42
2 parents 151e909 + af1406d
commit 01a7b42
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diff --git 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
@@ -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
@@ -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.                                                                  |