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Merge fast processes #259

Merged
merged 26 commits into from
Jan 27, 2025
Merged

Merge fast processes #259

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8181975
fix vep workflow inefficiency
nvnieuwk Jan 22, 2025
3b77dc8
fix an issue with the vep subwf
nvnieuwk Jan 22, 2025
00d1d00
fix vcfanno output
nvnieuwk Jan 23, 2025
df05e7d
update filter subworkflow
nvnieuwk Jan 23, 2025
5af2749
update ped filter subwf
nvnieuwk Jan 23, 2025
465d7b2
remove all tabix from vcf_annotation
nvnieuwk Jan 23, 2025
8f1380e
remove tabix from concat subwf
nvnieuwk Jan 23, 2025
afdbd04
remove tabix from vcfanno subwf
nvnieuwk Jan 23, 2025
3d144c4
remove mentions of tabix in subwfs
nvnieuwk Jan 23, 2025
15c34c7
bye bye unused tabix modules
nvnieuwk Jan 23, 2025
0736854
fix linting
nvnieuwk Jan 23, 2025
dcb5e73
Merge branch 'dev' into merge-fast-processes
nvnieuwk Jan 23, 2025
74ff865
Merge branch 'dev' into merge-fast-processes
nvnieuwk Jan 23, 2025
912a7a2
bump to dev
nvnieuwk Jan 23, 2025
cea2dfe
merge filter_beds and bedtools_intersect into process_beds
nvnieuwk Jan 23, 2025
0079ac4
fix first batch of tests
nvnieuwk Jan 23, 2025
51a9333
fix tests part2
nvnieuwk Jan 23, 2025
e1637d0
fix linting
nvnieuwk Jan 23, 2025
1e47527
fix more tests
nvnieuwk Jan 23, 2025
a081dd9
fix one more test
nvnieuwk Jan 23, 2025
cc2c294
bump vep
nvnieuwk Jan 24, 2025
eeb3358
fix vep stub
nvnieuwk Jan 24, 2025
14f5d02
merge filter steps
nvnieuwk Jan 24, 2025
ff36dcb
fix linting
nvnieuwk Jan 24, 2025
6646aa9
fix vep snap
nvnieuwk Jan 24, 2025
6836a7a
update changelog
nvnieuwk Jan 24, 2025
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remove mentions of tabix in subwfs
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@nvnieuwk
nvnieuwk committed Jan 23, 2025
commit 3d144c4ac10560725ef0385e2524cb692d733a83
1 change: 0 additions & 1 deletion subworkflows/local/vcf_filter_bcftools/main.nf
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Expand Up @@ -4,7 +4,6 @@

include { BCFTOOLS_FILTER as FILTER_1 } from '../../../modules/nf-core/bcftools/filter/main'
include { BCFTOOLS_FILTER as FILTER_2 } from '../../../modules/nf-core/bcftools/filter/main'
include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main'

workflow VCF_FILTER_BCFTOOLS {
take:
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3 changes: 0 additions & 3 deletions workflows/germline.nf
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Expand Up @@ -44,12 +44,9 @@ include { UNTAR } from '../
include { ENSEMBLVEP_DOWNLOAD } from '../modules/nf-core/ensemblvep/download/main'
include { BCFTOOLS_STATS } from '../modules/nf-core/bcftools/stats/main'
include { BCFTOOLS_NORM } from '../modules/nf-core/bcftools/norm/main'
include { TABIX_TABIX as TABIX_DECOMPOSE } from '../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_NORMALIZE } from '../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_DBSNP } from '../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_GVCF } from '../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_TRUTH } from '../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_FINAL } from '../modules/nf-core/tabix/tabix/main'
include { BCFTOOLS_STATS as BCFTOOLS_STATS_FAMILY } from '../modules/nf-core/bcftools/stats/main'
include { VCF2DB } from '../modules/nf-core/vcf2db/main'
include { MULTIQC } from '../modules/nf-core/multiqc/main'
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