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ramprasadnramprasadn
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update parameter name
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‎CHANGELOG.md

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@@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- A new parameter `concatenate_snv_calls` to generate a concatenated VCF file containing unannotated nuclear & mitochondrial SNV calls [#699](https://github.com/nf-core/raredisease/pull/699)
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- Functionality to check contamination in samples using VerifyBamID2 [#701](https://github.com/nf-core/raredisease/pull/701)
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- New parameters `svd_bed`, `svd_mu`, and `svd_ud` to supply reference files for VerifyBamID2 [#701](https://github.com/nf-core/raredisease/pull/701)
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- New parameters `verifybamid_svd_bed`, `verifybamid_svd_mu`, and `verifybamid_svd_ud` to supply reference files for VerifyBamID2 [#701](https://github.com/nf-core/raredisease/pull/701)
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### `Fixed`
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| Old parameter | New parameter |
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| ------------- | --------------------- |
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| | concatenate_snv_calls |
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| | svd_bed |
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| | svd_mu |
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| | svd_ud |
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| | verifybamid_svd_bed |
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| | verifybamid_svd_mu |
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| | verifybamid_svd_ud |
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### Tool updates
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| Tool | Old version | New version |
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| ------------ | ----------- | ----------- |
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| VerifyBamID2 | | 2.0.1 |
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## 2.4.0 - Vitalstatistix [2025-02-24]
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‎docs/output.md

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##### VerifyBamID2
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[VerifyBamID2](https://github.com/Griffan/VerifyBamID) is used to analyse a bam file and generates a contamination report. The pipeline will only generate the following files when the parameters `svd_bed`, `svd_mu`, and `svd_ud` are provided.
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[VerifyBamID2](https://github.com/Griffan/VerifyBamID) is used to analyse a bam file and generates a contamination report. The pipeline will only generate the following files when the parameters `verifybamid_svd_bed`, `verifybamid_svd_mu`, and `verifybamid_svd_ud` are provided.
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<details markdown="1">
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<summary>Output files</summary>

‎docs/usage.md

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##### 2. QC stats from the alignment files
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| Mandatory | Optional |
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| ------------------------------------------------------------ | ------------------- |
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| intervals_wgs<sup>1</sup> | |
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| intervals_y<sup>1</sup> | |
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| target_bed / (bait_intervals & target_intervals)<sup>2</sup> | |
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| | svd_bed<sup>3</sup> |
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| | svd_mu<sup>3</sup> |
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| | svd_ud<sup>3</sup> |
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| Mandatory | Optional |
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| ------------------------------------------------------------ | ------------------------------- |
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| intervals_wgs<sup>1</sup> | |
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| intervals_y<sup>1</sup> | |
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| target_bed / (bait_intervals & target_intervals)<sup>2</sup> | |
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| | verifybamid_svd_bed<sup>3</sup> |
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| | verifybamid_svd_mu<sup>3</sup> |
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| | verifybamid_svd_ud<sup>3</sup> |
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<sup>1</sup>These files are Picard's style interval list files, comprising the entire genome or only the chromosome Y. A version of these files for GRCh37 and for GRCh38 is supplied in the pipeline assets. These files are not necessary if you are using Sentieon.<br />
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<sup>2</sup> If a target_bed file is provided, bait_intervals and target_intervals can be generated by the pipeline.<br />

‎nextflow.config

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score_config_snv = null
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score_config_sv = null
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sdf = null
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svd_bed = null
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svd_mu = null
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svd_ud = null
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svdb_query_bedpedbs = null
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svdb_query_dbs = null
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target_bed = null
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variant_consequences_sv = null
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vep_filters = null
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vep_filters_scout_fmt = null
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verifybamid_svd_bed = null
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verifybamid_svd_mu = null
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verifybamid_svd_ud = null
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vcf2cytosure_blacklist = null
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vcfanno_extra_resources = null
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vcfanno_resources = null

‎nextflow_schema.json

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"help_text": "Optional file to rename sample ids in the vcf2cytosure vcf",
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"pattern": "^\\S+\\.csv$"
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},
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"svd_bed": {
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"verifybamid_svd_bed": {
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"type": "string",
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"exists": true,
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"format": "file-path",
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"description": "Path to a BED file containing markers used by verifybamid2.",
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"fa_icon": "fas fa-file-csv"
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},
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"svd_mu": {
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"verifybamid_svd_mu": {
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"type": "string",
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"exists": true,
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"format": "file-path",
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"description": "Path to mean matrix file of genotype matrix. Used by verifybamid2.",
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"fa_icon": "fas fa-file-csv"
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},
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"svd_ud": {
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"verifybamid_svd_ud": {
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"type": "string",
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"exists": true,
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"format": "file-path",

‎workflows/raredisease.nf

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: Channel.empty()
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ch_sv_bedpedbs = params.svdb_query_bedpedbs ? Channel.fromPath(params.svdb_query_bedpedbs)
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: Channel.empty()
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ch_svd_bed = params.svd_bed ? Channel.fromPath(params.svd_bed)
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ch_svd_bed = params.verifybamid_svd_bed ? Channel.fromPath(params.verifybamid_svd_bed)
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: Channel.empty()
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ch_svd_mu = params.svd_mu ? Channel.fromPath(params.svd_mu)
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ch_svd_mu = params.verifybamid_svd_mu ? Channel.fromPath(params.verifybamid_svd_mu)
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: Channel.empty()
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ch_svd_ud = params.svd_ud ? Channel.fromPath(params.svd_ud)
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ch_svd_ud = params.verifybamid_svd_ud ? Channel.fromPath(params.verifybamid_svd_ud)
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: Channel.empty()
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ch_target_bed = ch_references.target_bed
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ch_target_intervals = ch_references.target_intervals

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