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makes 0 an allowed value for sex #595

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Aug 14, 2024
Merged

makes 0 an allowed value for sex #595

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion assets/schema_input.json
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Expand Up @@ -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": {
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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -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. |
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