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Annotate and rank SNVs per family
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fellen31 committed Nov 12, 2024
1 parent 42ec814 commit 279ecc2
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4 changes: 4 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -89,6 +89,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#489](https://github.com/genomic-medicine-sweden/nallo/pull/489) - Updated nf-core template to 3.0.2
- [#493](https://github.com/genomic-medicine-sweden/nallo/pull/493) - Refactored `nallo.nf` to remove many nested ifs and easier to follow logic
- [#493](https://github.com/genomic-medicine-sweden/nallo/pull/493) - Updated rank_variants dependencies with sv_annotation
- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Changed to annotating and ranking SNVs per family instead of per project
- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Changed output documentation and structure to match `sample` and `family` for all variants

### `Removed`

Expand All @@ -97,6 +99,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#379](https://github.com/genomic-medicine-sweden/nallo/pull/379) - Removed VEP Plugins from testdata ([genomic-medicine-sweden/test-datasets#16](https://github.com/genomic-medicine-sweden/test-datasets/pull/16))
- [#388](https://github.com/genomic-medicine-sweden/nallo/pull/388) - Removed support for co-phasing SVs with HiPhase, as the officially supported caller (pbsv) is not in the pipeline
- [#412](https://github.com/genomic-medicine-sweden/nallo/pull/412) - Removed `bcftools/index`, as indexing is handled by other modules and no references remained. ([#377](https://github.com/genomic-medicine-sweden/nallo/issues/377))
- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Removed support for automatically creating an echvar database with SNVs and INDELs

### `Fixed`

Expand All @@ -107,6 +110,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#402](https://github.com/genomic-medicine-sweden/nallo/pull/402) - Fixed double sample names in HiFiCNV output
- [#438](https://github.com/genomic-medicine-sweden/nallo/pull/438) - Fixed missing/malformed software versions in `ADD_FOUND_IN_TAG`, `ADD_MOST_SEVERE_CSQ`, `ADD_MOST_SEVERE_PLI`, `SAMPLESHEET_PED`, `SOMALIER_PED` and `TRGT`
- [#444](https://github.com/genomic-medicine-sweden/nallo/pull/444) - Fixed genmod assigning wrong models on chromosome X when named `chrX` ([#343](https://github.com/genomic-medicine-sweden/nallo/issues/343))
- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Fixed genmod only scoring compounds in one family [#501](https://github.com/genomic-medicine-sweden/nallo/issues/501)

### Parameters

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2 changes: 1 addition & 1 deletion conf/modules/call_svs.config
Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ process {
'--write-index=tbi'
].join(' ')
publishDir = [
path: { "${params.outdir}/svs/single_sample/${meta.id}" },
path: { "${params.outdir}/svs/sample/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
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23 changes: 4 additions & 19 deletions conf/modules/general.config
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ process {
withName: '.*:NALLO:BCFTOOLS_STATS' {
ext.prefix = { "${vcf}" }
publishDir = [
path: { "${params.outdir}/snvs/stats/single_sample" },
path: { "${params.outdir}/snvs/stats/sample" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -51,7 +51,7 @@ process {
'--write-index=tbi'
].join(' ') }
publishDir = [
path: { "${params.outdir}/snvs/multi_sample/${meta.id}" },
path: { "${params.outdir}/snvs/family/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -64,7 +64,7 @@ process {
'--write-index=tbi'
].join(' ')
publishDir = [
path: { "${params.outdir}/snvs/single_sample/" },
path: { "${params.outdir}/snvs/sample/" },
mode: params.publish_dir_mode,
// Can't use prefix as it would come from the original file
saveAs: { filename ->
Expand All @@ -88,7 +88,7 @@ process {
'--write-index=tbi'
].join(' ')
publishDir = [
path: { "${params.outdir}/svs/single_sample/" },
path: { "${params.outdir}/svs/sample/" },
mode: params.publish_dir_mode,
// Can't use prefix as it would come from the original file
saveAs: { filename ->
Expand All @@ -111,13 +111,6 @@ process {
]
}

withName: '.*:NALLO:SOMALIER_PED' {
publishDir = [
path: { "${params.outdir}/pedigree/project/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]
}

withName: '.*:NALLO:SOMALIER_PED_FAMILY' {
publishDir = [
path: { "${params.outdir}/pedigree/family/" },
Expand Down Expand Up @@ -198,14 +191,6 @@ process {
]
}

withName: '.*:NALLO:ECHTVAR_ENCODE' {
publishDir = [
path: { "${params.outdir}/databases/echtvar/encode/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Summary
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