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Add option to skip haplogrep3 #675

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Merged
merged 1 commit into from
Feb 4, 2025
Merged

Add option to skip haplogrep3 #675

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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 option `skip_haplogrep3` to skip haplogrep3 [#675](https://github.com/nf-core/raredisease/pull/675)
- A new analysis option `mito` to call and annotate only mitochondrial variants [#608](https://github.com/nf-core/raredisease/pull/608)
- An option `extract_alignments` to restrict analysis to specific contigs [#644](https://github.com/nf-core/raredisease/pull/644)
- Fastp and ngsbits output files as input of MultiQC [#647](https://github.com/nf-core/raredisease/pull/647/).
Expand Down Expand Up @@ -40,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| ------------- | ------------------- |
| | extract_alignments |
| | restrict_to_contigs |
| | skip_haplogrep3 |

### Tool updates

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1 change: 1 addition & 0 deletions conf/test.config
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Expand Up @@ -31,6 +31,7 @@ params {
skip_mt_annotation = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip annotation on Github CI
skip_mt_subsample = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip subsample on Github CI
skip_peddy = true
skip_haplogrep3 = true

// Input data

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1 change: 1 addition & 0 deletions conf/test_sentieon.config
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Expand Up @@ -26,6 +26,7 @@ params {
// analysis params
skip_germlinecnvcaller = true
skip_peddy = true
skip_haplogrep3 = true

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_trio.csv'
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -33,6 +33,7 @@ params {
skip_fastp = false
skip_gens = true
skip_germlinecnvcaller = false
skip_haplogrep3 = false
skip_peddy = false
skip_me_calling = false
skip_me_annotation = false
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5 changes: 5 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -564,6 +564,11 @@
"description": "Specifies whether or not to skip CNV calling using GATK's GermlineCNVCaller",
"fa_icon": "fas fa-toggle-on"
},
"skip_haplogrep3": {
"type": "boolean",
"description": "Specifies whether or not to skip haplogrep3.",
"fa_icon": "fas fa-toggle-on"
},
"skip_peddy": {
"type": "boolean",
"description": "Specifies whether or not to skip peddy.",
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20 changes: 12 additions & 8 deletions subworkflows/local/annotate_mt_snvs.nf
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Expand Up @@ -31,6 +31,7 @@ workflow ANNOTATE_MT_SNVS {

main:
ch_versions = Channel.empty()
ch_haplog = Channel.empty()

// add prefix to meta
ch_mt_vcf
Expand Down Expand Up @@ -98,22 +99,25 @@ workflow ANNOTATE_MT_SNVS {

TABIX_TABIX_VEP_MT(ENSEMBLVEP_MT.out.vcf)

// Running haplogrep2
HAPLOGREP3_CLASSIFY_MT(ch_haplogrep_in)
// Running haplogrep3
if (!params.skip_haplogrep3) {
HAPLOGREP3_CLASSIFY_MT(ch_haplogrep_in)
ch_haplog = HAPLOGREP3_CLASSIFY_MT.out.txt
ch_versions = ch_versions.mix(HAPLOGREP3_CLASSIFY_MT.out.versions)
}

ch_versions = ch_versions.mix(ENSEMBLVEP_MT.out.versions)
ch_versions = ch_versions.mix(TABIX_TABIX_VEP_MT.out.versions)
ch_versions = ch_versions.mix(VCFANNO_MT.out.versions)
ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions)
ch_versions = ch_versions.mix(HAPLOGREP3_CLASSIFY_MT.out.versions)
ch_versions = ch_versions.mix(ZIP_TABIX_VCFANNO_MT.out.versions)
ch_versions = ch_versions.mix(ZIP_TABIX_HMTNOTE_MT.out.versions)
ch_versions = ch_versions.mix(REPLACE_SPACES_IN_VCFINFO.out.versions)

emit:
haplog = HAPLOGREP3_CLASSIFY_MT.out.txt // channel: [ val(meta), path(txt) ]
vcf_ann = ENSEMBLVEP_MT.out.vcf // channel: [ val(meta), path(vcf) ]
tbi = TABIX_TABIX_VEP_MT.out.tbi // channel: [ val(meta), path(tbi) ]
report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ]
versions = ch_versions // channel: [ path(versions.yml) ]
haplog = ch_haplog // channel: [ val(meta), path(txt) ]
vcf_ann = ENSEMBLVEP_MT.out.vcf // channel: [ val(meta), path(vcf) ]
tbi = TABIX_TABIX_VEP_MT.out.tbi // channel: [ val(meta), path(tbi) ]
report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ]
versions = ch_versions // channel: [ path(versions.yml) ]
}