Merge branch 'dev' of github.com:nf-core/raredisease into gatkcnvcaller

nf-core · Jul 7, 2023 · 2f83bbb · 2f83bbb
2 parents 66efabc + 4d37b19
commit 2f83bbb
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,10 @@ 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.

diff --git a/conf/modules/merge_annotate_MT.config b/conf/modules/merge_annotate_MT.config
@@ -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
         ]
     }
 

diff --git a/subworkflows/local/mitochondria/merge_annotate_MT.nf b/subworkflows/local/mitochondria/merge_annotate_MT.nf
@@ -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: