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Add a new paramter to skip sv calling #572

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Merged
merged 6 commits into from
Jun 24, 2024
Merged

Add a new paramter to skip sv calling #572

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7cc4bda
reorder sv bits
ramprasadn Jun 21, 2024
ad13478
Merge branch 'modularize-everything-1' into modularize-everything-2
ramprasadn Jun 21, 2024
cd7cd00
Merge branch 'dev' of github.com:nf-core/raredisease into modularize-…
ramprasadn Jun 24, 2024
90fad32
fix logic
ramprasadn Jun 24, 2024
f1ab55d
changelog
ramprasadn Jun 24, 2024
31e8f2e
fix error
ramprasadn Jun 24, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- A new parameter `skip_sv_calling` to skip sv calling workflow [#572](https://github.com/nf-core/raredisease/pull/572)
- Two new parameters `skip_snv_calling` and `skip_repeat_analysis` to skip snv calling and repeat analysis respectively [#571](https://github.com/nf-core/raredisease/pull/571)
- Two new parameters `mbuffer_mem` and `samtools_sort_threads` to control resources given to mbuffer and samtools sort in the bwameme module [#570](https://github.com/nf-core/raredisease/pull/570)

Expand All @@ -27,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| | samtools_sort_threads |
| | skip_repeat_analysis |
| | skip_snv_calling |
| | skip_sv_calling |

## 2.1.0 - Obelix [2024-05-29]

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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -42,6 +42,7 @@ params {
skip_snv_annotation = false
skip_snv_calling = false
skip_sv_annotation = false
skip_sv_calling = false
skip_mt_subsample = false
skip_vcf2cytosure = true
skip_vep_filter = false
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5 changes: 5 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -588,6 +588,11 @@
"description": "Specifies whether or not to skip annotate structural variant subworkflow.",
"fa_icon": "fas fa-toggle-on"
},
"skip_sv_calling": {
"type": "boolean",
"description": "Specifies whether or not to skip nuclear and mitochondrial SV calling and annotation.",
"fa_icon": "fas fa-toggle-on"
},
"skip_vcf2cytosure": {
"type": "boolean",
"default": true,
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