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Avoid publishing uncompressed VCF-file from HMTNOTE_ANNOTATE #368

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merged 5 commits into from
Jul 6, 2023
Merged

Avoid publishing uncompressed VCF-file from HMTNOTE_ANNOTATE #368

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4cc9527
Only publishing compressed vcf from HMTNOTE_ANNOTATE not uncompressed
asp8200 Jun 29, 2023
0cb3e4e
Removing redundant rename of imported module
asp8200 Jun 29, 2023
b41676f
Merge branch 'dev' into compress_output
asp8200 Jul 6, 2023
faff494
Updating changelog
asp8200 Jul 6, 2023
e8599cd
Merge branch 'compress_output' of https://github.com/asp8200/raredise…
asp8200 Jul 6, 2023
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- eKLIPse to identify large mitochondrial deletions [#365](https://github.com/nf-core/raredisease/pull/365)
- UPD+Chromograph to identify and visualize UPD sites and regions in the chromosomes [#364](https://github.com/nf-core/raredisease/pull/364) and [#366](https://github.com/nf-core/raredisease/pull/366)

### Fixed

- Avoiding publishing uncompressed VCF-file from `HMTNOTE_ANNOTATE`. (The corresponding compressed VCF-file still gets published.) [#368](https://github.com/nf-core/raredisease/pull/368)

## v1.0.0 - [2023-06-01]

Initial release of nf-core/raredisease, created with the [nf-core](https://nf-co.re/) template.
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5 changes: 1 addition & 4 deletions conf/modules/merge_annotate_MT.config
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Expand Up @@ -71,10 +71,7 @@ process {
ext.prefix = { "${meta.id}_vep_vcfanno_hmtnote_mt" }
ext.args = '--offline'
publishDir = [
path: { "${params.outdir}/annotate_mt" },
mode: params.publish_dir_mode,
pattern: "*{vcf}",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
enabled: false
]
}

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2 changes: 1 addition & 1 deletion subworkflows/local/mitochondria/merge_annotate_MT.nf
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Expand Up @@ -16,7 +16,7 @@ include { HAPLOGREP2_CLASSIFY as HAPLOGREP2_CLASSIFY_MT } from '../../..
include { VCFANNO as VCFANNO_MT } from '../../../modules/nf-core/vcfanno/main'
include { ANNOTATE_CADD } from '../annotation/annotate_cadd'
include { TABIX_BGZIPTABIX as ZIP_TABIX_HMTNOTE } from '../../../modules/nf-core/tabix/bgziptabix/main'
include { HMTNOTE_ANNOTATE as HMTNOTE_ANNOTATE } from '../../../modules/nf-core/hmtnote/annotate/main'
include { HMTNOTE_ANNOTATE } from '../../../modules/nf-core/hmtnote/annotate/main'

workflow MERGE_ANNOTATE_MT {
take:
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