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replace local subworkflow with nf-core version - vcf_annotate_ensemblvep #865

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merged 16 commits into from
Nov 25, 2022
Merged

replace local subworkflow with nf-core version - vcf_annotate_ensemblvep #865

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67f8099
nf-core subworfklows install vcf_annotate_ensemblvep
maxulysse Nov 24, 2022
587d261
update test tags
maxulysse Nov 24, 2022
c881d37
update CHANGELOG
maxulysse Nov 24, 2022
21b3557
fix section for items in CHANGELOG
maxulysse Nov 24, 2022
cd735b0
nf-core subworkflows update vcf_annotate_ensemblvep
maxulysse Nov 25, 2022
66b6d17
Merge branch 'dev' into dev_vcf_annotate_ensemblvep
maxulysse Nov 25, 2022
14c9e37
[automated] Fix linting with Prettier
nf-core-bot Nov 25, 2022
599d262
update output files
maxulysse Nov 25, 2022
de712a0
update igenomes tags for vep
maxulysse Nov 25, 2022
7d964e7
fix hash
maxulysse Nov 25, 2022
776e661
update files
maxulysse Nov 25, 2022
a9a2942
add dependencies update
maxulysse Nov 25, 2022
8a5d091
update tests
maxulysse Nov 25, 2022
cf8a58e
fix content of summary
maxulysse Nov 25, 2022
4678652
fix tests
maxulysse Nov 25, 2022
e9921ab
prettier
maxulysse Nov 25, 2022
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12 changes: 9 additions & 3 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@
},
"bcftools/mpileup": {
"branch": "master",
"git_sha": "6301e29d77e7ec7ce98b55b8a361b316a9a91bfe"
"git_sha": "6301e29d77e7ec7ce98b55b8a361b316a9a91bfe",
"installed_by": ["modules"]
},
"bcftools/sort": {
"branch": "master",
Expand Down Expand Up @@ -119,7 +120,7 @@
"ensemblvep": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": ["modules"]
"installed_by": ["modules", "vcf_annotate_ensemblvep"]
},
"fastp": {
"branch": "master",
Expand Down Expand Up @@ -386,7 +387,7 @@
"tabix/bgziptabix": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": ["modules", "vcf_annotate_snpeff"]
"installed_by": ["modules", "vcf_annotate_snpeff", "vcf_annotate_ensemblvep"]
},
"tabix/tabix": {
"branch": "master",
Expand Down Expand Up @@ -417,6 +418,11 @@
},
"subworkflows": {
"nf-core": {
"vcf_annotate_ensemblvep": {
"branch": "master",
"git_sha": "8c343b3c8a0925949783dc547666007c245c235b",
"installed_by": ["subworkflows"]
},
"vcf_annotate_snpeff": {
"branch": "master",
"git_sha": "df47164506202e7b994825a9bcd38d2ca5954e1a",
Expand Down
6 changes: 3 additions & 3 deletions subworkflows/local/vcf_annotate_all/main.nf
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Expand Up @@ -2,9 +2,9 @@
// ANNOTATION
//

include { VCF_ANNOTATE_ENSEMBLVEP } from '../vcf_annotate_ensemblvep/main'
include { VCF_ANNOTATE_ENSEMBLVEP as VCF_ANNOTATE_MERGE } from '../vcf_annotate_ensemblvep/main'
include { VCF_ANNOTATE_SNPEFF } from '../../nf-core/vcf_annotate_snpeff/main'
include { VCF_ANNOTATE_ENSEMBLVEP } from '../../nf-core/vcf_annotate_ensemblvep/main.nf'
include { VCF_ANNOTATE_ENSEMBLVEP as VCF_ANNOTATE_MERGE } from '../../nf-core/vcf_annotate_ensemblvep/main.nf'
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include { VCF_ANNOTATE_SNPEFF } from '../../nf-core/vcf_annotate_snpeff/main.nf'

workflow VCF_ANNOTATE_ALL {
take:
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29 changes: 0 additions & 29 deletions subworkflows/local/vcf_annotate_ensemblvep/meta.yml
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This file was deleted.

10 changes: 5 additions & 5 deletions ...ows/local/vcf_annotate_ensemblvep/main.nf → ...s/nf-core/vcf_annotate_ensemblvep/main.nf
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61 changes: 61 additions & 0 deletions subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml
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4 changes: 2 additions & 2 deletions tests/config/pytest_tags.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -244,7 +244,7 @@ merge:
- modules/nf-core/snpeff/main.nf
- modules/nf-core/tabix/bgziptabix/main.nf
- subworkflows/local/vcf_annotate_all/main.nf
- subworkflows/local/vcf_annotate_ensemblvep/main.nf
- subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf
- subworkflows/nf-core/vcf_annotate_snpeff/main.nf

## snpeff
Expand All @@ -259,4 +259,4 @@ vep:
- conf/modules/annotate.config
- modules/nf-core/ensemblvep/main.nf
- modules/nf-core/tabix/bgziptabix/main.nf
- subworkflows/local/vcf_annotate_ensemblvep/main.nf
- subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf