From 4cc952775743391368a9d6aa731bc1154c0a5a2c Mon Sep 17 00:00:00 2001
From: asp8200 <anders@mynucleus.com>
Date: Thu, 29 Jun 2023 13:01:58 +0000
Subject: [PATCH 1/3] Only publishing compressed vcf from HMTNOTE_ANNOTATE not
 uncompressed

---
 conf/modules/merge_annotate_MT.config | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/conf/modules/merge_annotate_MT.config b/conf/modules/merge_annotate_MT.config
index 0ca97ca6..027c6805 100644
--- 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
         ]
     }
 

From 0cb3e4e67b9a5231fdf7cc8aaf51099ae284eb86 Mon Sep 17 00:00:00 2001
From: asp8200 <anders@mynucleus.com>
Date: Thu, 29 Jun 2023 13:02:28 +0000
Subject: [PATCH 2/3] Removing redundant rename of imported module

---
 subworkflows/local/mitochondria/merge_annotate_MT.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/mitochondria/merge_annotate_MT.nf b/subworkflows/local/mitochondria/merge_annotate_MT.nf
index eee3f199..8a78ed27 100644
--- 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:

From faff4947abbb24ba2fe5602cd871ebac24e73477 Mon Sep 17 00:00:00 2001
From: asp8200 <anders@mynucleus.com>
Date: Thu, 6 Jul 2023 12:04:22 +0000
Subject: [PATCH 3/3] Updating changelog

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 13232758..074807bd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -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.