+
Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Changed`

- Refactored code to only handle clinical variants in the generate_clinical_set workflow [#693](https://github.com/nf-core/raredisease/pull/693)
- Updated `add_most_severe_consequence` and `add_most_severe_pli` to fix spelling and language server warnings [#689](https://github.com/nf-core/raredisease/pull/689)
- Refactored code to address issues highlighted by language server [#688](https://github.com/nf-core/raredisease/pull/688)
- Changed for loop to each in create_pedigree_file [#683](https://github.com/nf-core/raredisease/pull/683)
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/local/annotate_mobile_elements.nf
Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,6 @@ workflow ANNOTATE_MOBILE_ELEMENTS {
ch_versions = ch_versions.mix( BCFTOOLS_VIEW_FILTER.out.versions )

emit:
vcf = BCFTOOLS_VIEW_FILTER.out.vcf // channel: [ val(meta), path(vcf) ]
vcf_ann = BCFTOOLS_VIEW_FILTER.out.vcf // channel: [ val(meta), path(vcf) ]
versions = ch_versions // channel: [ path(versions.yml) ]
}
1 change: 0 additions & 1 deletion subworkflows/local/annotate_mt_snvs.nf
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,6 @@ workflow ANNOTATE_MT_SNVS {
main:
ch_versions = Channel.empty()
ch_haplog = Channel.empty()
ch_haplogrep_in = Channel.empty()

// add prefix to meta
ch_mt_vcf
Expand Down
22 changes: 3 additions & 19 deletions subworkflows/local/generate_clinical_set.nf
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@

include { ENSEMBLVEP_FILTERVEP } from '../../modules/nf-core/ensemblvep/filtervep'
include { TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip'
include { TABIX_TABIX } from '../../modules/nf-core/tabix/tabix'
include { BCFTOOLS_FILTER } from '../../modules/nf-core/bcftools/filter'

workflow GENERATE_CLINICAL_SET {
Expand All @@ -16,15 +15,8 @@ workflow GENERATE_CLINICAL_SET {
main:
ch_versions = Channel.empty()

ch_vcf
.multiMap { meta, vcf ->
clinical: [ meta + [ set: "clinical" ], vcf ]
research: [ meta + [ set: "research" ], vcf ]
}
.set { ch_clin_research_vcf }

ENSEMBLVEP_FILTERVEP(
ch_clin_research_vcf.clinical,
ch_vcf,
ch_hgnc_ids
)
.output
Expand All @@ -40,17 +32,9 @@ workflow GENERATE_CLINICAL_SET {
ch_versions = ch_versions.mix( TABIX_BGZIP.out.versions )
}

ch_clin_research_vcf.research
.mix( ch_clinical )
.set { ch_clin_research_split }

TABIX_TABIX( ch_clin_research_split )

ch_versions = ch_versions.mix( ENSEMBLVEP_FILTERVEP.out.versions )
ch_versions = ch_versions.mix( TABIX_TABIX.out.versions )

emit:
vcf = ch_clin_research_split // channel: [ val(meta), path(vcf) ]
tbi = TABIX_TABIX.out.tbi // channel: [ val(meta), path(tbi) ]
versions = ch_versions // channel: [ path(versions.yml) ]
vcf = ch_clinical // channel: [ val(meta), path(vcf) ]
versions = ch_versions // channel: [ path(versions.yml) ]
}
50 changes: 42 additions & 8 deletions workflows/raredisease.nf
Original file line number Diff line number Diff line change
Expand Up @@ -496,15 +496,23 @@ workflow RAREDISEASE {
).set { ch_snv_annotate }
ch_versions = ch_versions.mix(ch_snv_annotate.versions)

ch_snv_annotate.vcf_ann
.multiMap { meta, vcf ->
clinical: [ meta + [ set: "clinical" ], vcf ]
research: [ meta + [ set: "research" ], vcf ]
}
.set { ch_clin_research_snv_vcf }

GENERATE_CLINICAL_SET_SNV(
ch_snv_annotate.vcf_ann,
ch_clin_research_snv_vcf.clinical,
ch_hgnc_ids,
false
)
ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SNV.out.versions)

ch_ann_csq_snv_in = GENERATE_CLINICAL_SET_SNV.out.vcf.mix(ch_clin_research_snv_vcf.research)
ANN_CSQ_PLI_SNV (
GENERATE_CLINICAL_SET_SNV.out.vcf,
ch_ann_csq_snv_in,
ch_variant_consequences_snv
)
ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions)
Expand Down Expand Up @@ -549,15 +557,23 @@ workflow RAREDISEASE {
).set { ch_mt_annotate }
ch_versions = ch_versions.mix(ch_mt_annotate.versions)

ch_mt_annotate.vcf_ann
.multiMap { meta, vcf ->
clinical: [ meta + [ set: "clinical" ], vcf ]
research: [ meta + [ set: "research" ], vcf ]
}
.set { ch_clin_research_mt_vcf }

GENERATE_CLINICAL_SET_MT(
ch_mt_annotate.vcf_ann,
ch_clin_research_mt_vcf.clinical,
ch_hgnc_ids,
true
)
ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_MT.out.versions)

ch_ann_csq_mtsnv_in = GENERATE_CLINICAL_SET_MT.out.vcf.mix(ch_clin_research_mt_vcf.research)
ANN_CSQ_PLI_MT(
GENERATE_CLINICAL_SET_MT.out.vcf,
ch_ann_csq_mtsnv_in,
ch_variant_consequences_snv
)
ch_versions = ch_versions.mix(ANN_CSQ_PLI_MT.out.versions)
Expand Down Expand Up @@ -625,15 +641,24 @@ workflow RAREDISEASE {
).set { ch_sv_annotate }
ch_versions = ch_versions.mix(ch_sv_annotate.versions)

ch_sv_annotate.vcf_ann
.multiMap { meta, vcf ->
clinical: [ meta + [ set: "clinical" ], vcf ]
research: [ meta + [ set: "research" ], vcf ]
}
.set { ch_clin_research_sv_vcf }

GENERATE_CLINICAL_SET_SV(
ch_sv_annotate.vcf_ann,
ch_clin_research_sv_vcf.clinical,
ch_hgnc_ids,
false
)
ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SV.out.versions)

ch_ann_csq_sv_in = GENERATE_CLINICAL_SET_SV.out.vcf.mix(ch_clin_research_sv_vcf.research)

ANN_CSQ_PLI_SV (
GENERATE_CLINICAL_SET_SV.out.vcf,
ch_ann_csq_sv_in,
ch_variant_consequences_sv
)
ch_versions = ch_versions.mix(ANN_CSQ_PLI_SV.out.versions)
Expand Down Expand Up @@ -684,16 +709,25 @@ workflow RAREDISEASE {
params.genome,
params.vep_cache_version,
ch_vep_extra_files
)
).set { ch_me_annotate }
ch_versions = ch_versions.mix(ANNOTATE_MOBILE_ELEMENTS.out.versions)

ch_me_annotate.vcf_ann
.multiMap { meta, vcf ->
clinical: [ meta + [ set: "clinical" ], vcf ]
research: [ meta + [ set: "research" ], vcf ]
}
.set { ch_clin_research_me_vcf }

GENERATE_CLINICAL_SET_ME(
ANNOTATE_MOBILE_ELEMENTS.out.vcf,
ch_clin_research_me_vcf.clinical,
ch_hgnc_ids,
false
)
ch_versions = ch_versions.mix( GENERATE_CLINICAL_SET_ME.out.versions )

ch_ann_csq_me_in = GENERATE_CLINICAL_SET_ME.out.vcf.mix(ch_clin_research_me_vcf.research)

ANN_CSQ_PLI_ME(
GENERATE_CLINICAL_SET_ME.out.vcf,
ch_variant_consequences_sv
Expand Down
点击 这是indexloc提供的php浏览器服务,不要输入任何密码和下载