From 178cc0ff089b7f616bf764b308dbf614cb4bbc23 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 20 Dec 2022 11:02:53 +0100
Subject: [PATCH 01/29] updates tiddit

---
 CHANGELOG.md                       | 7 +++++++
 definitions/rd_dna_parameters.yaml | 2 +-
 lib/MIP/Constants.pm               | 2 +-
 templates/mip_install_config.yaml  | 4 ++--
 4 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 305ec7aa5..802de3669 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,13 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## Develop
+
+Changes sv annotation overlap back to 0.8 (from 0.5) with the new tiddit update
+### Tools
+
+Tiddit 3.3.2 -> 3.4.0
+
 ## [11.1.1]
 
 - Updates chromgraph to version 1.3.1
diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
index f6d96dccb..1a3240afd 100755
--- a/definitions/rd_dna_parameters.yaml
+++ b/definitions/rd_dna_parameters.yaml
@@ -1001,7 +1001,7 @@ sv_svdb_query_overlap:
   associated_recipe:
     - sv_annotate
   data_type: SCALAR
-  default: 0.5
+  default: 0.8
   type: recipe_argument
 sv_vcfanno_config:
   associated_recipe:
diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
index 71547bd02..3fadd84df 100644
--- a/lib/MIP/Constants.pm
+++ b/lib/MIP/Constants.pm
@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{11.1.1};
+Readonly our $MIP_VERSION => q{11.1.1-develop};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index f25b6ddb6..2e1365c53 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -125,7 +125,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:v11.1.1
+    uri: docker.io/clinicalgenomics/mip:develop
   multiqc:
     executable:
       multiqc:
@@ -221,7 +221,7 @@ container:
   tiddit:
     executable:
       tiddit:
-    uri: quay.io/biocontainers/tiddit:3.3.2--py39h5094d80_0
+    uri: quay.io/repository/biocontainers/tiddit:3.4.0--py310hc2b7f4b_0
   trim-galore:
     executable:
       trim_galore:

From 33496460232541cce92768aaf0bcb3ba9b2656a6 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 20 Dec 2022 11:50:27 +0100
Subject: [PATCH 02/29] fix path to tiddit container

---
 templates/mip_install_config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index 2e1365c53..00928fb08 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -221,7 +221,7 @@ container:
   tiddit:
     executable:
       tiddit:
-    uri: quay.io/repository/biocontainers/tiddit:3.4.0--py310hc2b7f4b_0
+    uri: quay.io/biocontainers/tiddit:3.4.0--py310hc2b7f4b_0
   trim-galore:
     executable:
       trim_galore:

From 6e1e35bcc13b68939028966b457b0bc0287f2f87 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 20 Dec 2022 12:06:27 +0100
Subject: [PATCH 03/29] changed mip develop version syntax

---
 lib/MIP/Constants.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
index 3fadd84df..8f8c7e6ad 100644
--- a/lib/MIP/Constants.pm
+++ b/lib/MIP/Constants.pm
@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{11.1.1-develop};
+Readonly our $MIP_VERSION => q{11.1.2};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

From ecc7bf52e8037915d711340fa20ab362af697bc0 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Thu, 22 Dec 2022 10:48:51 +0100
Subject: [PATCH 04/29] updates variant catalog for expansionhunter

---
 CHANGELOG.md                                  |  4 ++
 definitions/rd_dna_parameters.yaml            |  2 +-
 lib/MIP/Constants.pm                          |  2 +-
 ...pansionhunter_variant_catalog_-4.0.2-.json |  0
 .../mip_download_rd_dna_config_-1.0-.yaml     | 45 +++++++------------
 templates/mip_install_config.yaml             |  2 +-
 6 files changed, 22 insertions(+), 33 deletions(-)
 delete mode 100644 t/data/references/grch37_expansionhunter_variant_catalog_-4.0.2-.json

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 305ec7aa5..0a88f165e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## Develop
+
+Updates expansionhunter variant catalog
+
 ## [11.1.1]
 
 - Updates chromgraph to version 1.3.1
diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
index f6d96dccb..7e38d9c7b 100755
--- a/definitions/rd_dna_parameters.yaml
+++ b/definitions/rd_dna_parameters.yaml
@@ -866,7 +866,7 @@ expansionhunter_variant_catalog_file_path:
   associated_recipe:
     - expansionhunter
   data_type: SCALAR
-  default: grch37_expansionhunter_variant_catalog_-4.0.2-.json
+  default: grch37_expansionhunter_variant_catalog_-5.0.0-.json
   exists_check: file
   is_reference: 1
   reference: reference_dir
diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
index 71547bd02..8f8c7e6ad 100644
--- a/lib/MIP/Constants.pm
+++ b/lib/MIP/Constants.pm
@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{11.1.1};
+Readonly our $MIP_VERSION => q{11.1.2};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;
diff --git a/t/data/references/grch37_expansionhunter_variant_catalog_-4.0.2-.json b/t/data/references/grch37_expansionhunter_variant_catalog_-4.0.2-.json
deleted file mode 100644
index e69de29bb..000000000
diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml
index e5daeb2e6..585795270 100644
--- a/templates/mip_download_rd_dna_config_-1.0-.yaml
+++ b/templates/mip_download_rd_dna_config_-1.0-.yaml
@@ -41,9 +41,8 @@ reference:
     - 20150915
     - 20200310
   expansionhunter:
-    - 3.0.1
-    - 3.1.2
     - 4.0.2
+    - 5.0.0
   gatk_mitochondrial_ref:
     - v0_m_amb
     - v0_m_ann
@@ -445,20 +444,6 @@ reference_feature:
         url_prefix: https://raw.githubusercontent.com/dellytools/delly/master/excludeTemplates/
   expansionhunter:
     grch37:
-      3.0.1:
-        file: variant_catalog_grch37.json
-        file_check: variant_catalog_grch37.json.md5
-        outfile: grch37_expansionhunter_variant_catalog_-3.0.1-.json
-        outfile_check: grch37_expansionhunter_variant_catalog_-3.0.1-.json.md5
-        outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v3.0.1/
-      3.1.2:
-        file: variant_catalog_grch37.json
-        file_check: variant_catalog_grch37.json.md5
-        outfile: grch37_expansionhunter_variant_catalog_-3.1.2-.json
-        outfile_check: grch37_expansionhunter_variant_catalog_-3.1.2-.json.md5
-        outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v3.1.2/
       4.0.2:
         file: variant_catalog_grch37.json
         file_check: variant_catalog_grch37.json.md5
@@ -466,21 +451,14 @@ reference_feature:
         outfile_check: grch37_expansionhunter_variant_catalog_-4.0.2-.json.md5
         outfile_check_method: md5sum
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v4.0.2/
-    grch38:
-      3.0.1:
-        file: variant_catalog_grch38.json
-        file_check: variant_catalog_grch38.json.md5
-        outfile: grch38_expansionhunter_variant_catalog_-3.0.1-.json
-        outfile_check: grch38_expansionhunter_variant_catalog_-3.0.1-.json.md5
-        outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v3.0.1/
-      3.1.2:
-        file: variant_catalog_hg38.json
-        file_check: variant_catalog_hg38.json.md5
-        outfile: grch38_expansionhunter_variant_catalog_-3.1.2-.json
-        outfile_check: grch38_expansionhunter_variant_catalog_-3.1.2-.json.md5
+      5.0.0:
+        file: variant_catalog_grch37.json
+        file_check: variant_catalog_grch37.json.md5
+        outfile: grch37_expansionhunter_variant_catalog_-5.0.0-.json
+        outfile_check: grch37_expansionhunter_variant_catalog_-5.0.0-.json.md5
         outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v3.1.2/
+        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v5.0.0/
+    grch38:
       4.0.2:
         file: variant_catalog_hg38.json
         file_check: variant_catalog_hg38.json.md5
@@ -488,6 +466,13 @@ reference_feature:
         outfile_check: grch38_expansionhunter_variant_catalog_-4.0.2-.json.md5
         outfile_check_method: md5sum
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v4.0.2/
+      5.0.0:
+        file: variant_catalog_hg38.json
+        file_check: variant_catalog_hg38.json.md5
+        outfile: grch38_expansionhunter_variant_catalog_-5.0.0-.json
+        outfile_check: grch38_expansionhunter_variant_catalog_-5.0.0-.json.md5
+        outfile_check_method: md5sum
+        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v5.0.0/
   gatk_mitochondrial_ref:
     grch38:
       v0_m_amb:
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index f25b6ddb6..74ddfd61e 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -125,7 +125,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:v11.1.1
+    uri: docker.io/clinicalgenomics/mip:develop
   multiqc:
     executable:
       multiqc:

From 9006464b740c3fe922644f75150784a76a2b98c5 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Thu, 22 Dec 2022 11:00:22 +0100
Subject: [PATCH 05/29] added test data file

---
 .../grch37_expansionhunter_variant_catalog_-5.0.0-.json           | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 t/data/references/grch37_expansionhunter_variant_catalog_-5.0.0-.json

diff --git a/t/data/references/grch37_expansionhunter_variant_catalog_-5.0.0-.json b/t/data/references/grch37_expansionhunter_variant_catalog_-5.0.0-.json
new file mode 100644
index 000000000..e69de29bb

From e62b681e11b0a1f8e5a81e2488dded400ad70412 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Thu, 5 Jan 2023 11:47:55 +0100
Subject: [PATCH 06/29] bump memory for salmon quant

---
 CHANGELOG.md                       | 4 ++++
 definitions/rd_rna_parameters.yaml | 2 +-
 lib/MIP/Constants.pm               | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 305ec7aa5..53debb434 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## Develop
+
+- Increased memory allocation for salmon
+
 ## [11.1.1]
 
 - Updates chromgraph to version 1.3.1
diff --git a/definitions/rd_rna_parameters.yaml b/definitions/rd_rna_parameters.yaml
index 685b904ec..31c7ec923 100755
--- a/definitions/rd_rna_parameters.yaml
+++ b/definitions/rd_rna_parameters.yaml
@@ -194,7 +194,7 @@ recipe_memory:
     picardtools_mergesamfiles: 5
     preseq_ar: 8
     rseqc: 40
-    salmon_quant: 2
+    salmon_quant: 4
     star_aln: 5
     star_fusion: 25
     stringtie_ar: 2
diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
index 71547bd02..8f8c7e6ad 100644
--- a/lib/MIP/Constants.pm
+++ b/lib/MIP/Constants.pm
@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{11.1.1};
+Readonly our $MIP_VERSION => q{11.1.2};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

From b6f71fd3c77372bde5dbdf29f415ddb36fec6734 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Mon, 9 Jan 2023 14:26:33 +0100
Subject: [PATCH 07/29] increase mem for picardtools mergesamfiles

---
 CHANGELOG.md                       | 2 +-
 definitions/rd_rna_parameters.yaml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e6434c497..ea175b54a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ## Develop
 
-- Increased memory allocation for salmon
+- Increased memory allocation for salmon and picardtools_mergersamfiles (RNA)
 - Updates expansionhunter variant catalog
 - Changes sv annotation overlap back to 0.8 (from 0.5) with the new tiddit update
 
diff --git a/definitions/rd_rna_parameters.yaml b/definitions/rd_rna_parameters.yaml
index 31c7ec923..52d43d54c 100755
--- a/definitions/rd_rna_parameters.yaml
+++ b/definitions/rd_rna_parameters.yaml
@@ -191,7 +191,7 @@ recipe_memory:
     merge_fusion_reports: 8
     multiqc_ar: 10
     picardtools_collectrnaseqmetrics: 10
-    picardtools_mergesamfiles: 5
+    picardtools_mergesamfiles: 8
     preseq_ar: 8
     rseqc: 40
     salmon_quant: 4

From 2d1cc43deab74ea87d6d9c9b1026cfbc64729ef2 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 10 Jan 2023 08:24:22 +0100
Subject: [PATCH 08/29] updates megafusion

---
 CHANGELOG.md                      | 4 +++-
 containers/megafusion/Dockerfile  | 4 ++--
 templates/mip_install_config.yaml | 2 +-
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ea175b54a..12302120f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,10 +8,12 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Increased memory allocation for salmon and picardtools_mergersamfiles (RNA)
 - Updates expansionhunter variant catalog
 - Changes sv annotation overlap back to 0.8 (from 0.5) with the new tiddit update
+- New version of MegaFusion. A bug in the previous version prevented SVDB from writing the format and sample field in the vcf.
 
 ### Tools
 
-Tiddit 3.3.2 -> 3.4.0
+- Tiddit 3.3.2 -> 3.4.0
+- MegaFusion 66a3a80 -> d3feacf
 
 ## [11.1.1]
 
diff --git a/containers/megafusion/Dockerfile b/containers/megafusion/Dockerfile
index 60fd98924..dbb778bc8 100644
--- a/containers/megafusion/Dockerfile
+++ b/containers/megafusion/Dockerfile
@@ -7,7 +7,7 @@ FROM clinicalgenomics/mip_base:2.1
 LABEL base_image="clinicalgenomics/mip_base:2.1"
 LABEL version="4"
 LABEL software="MegaFusion"
-LABEL software.version="66a3a80"
+LABEL software.version="d3feacf"
 LABEL extra.binaries="MegaFusion.py"
 LABEL maintainer="Clinical-Genomics/MIP"
 
@@ -25,5 +25,5 @@ RUN git clone https://github.com/J35P312/MegaFusion.git /opt/conda/share/MegaFus
 WORKDIR /opt/conda/share/MegaFusion
 
 ## Make sure we're on the right commit
-RUN git reset --hard 66a3a80
+RUN git reset --hard d3feacf
 
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index 00928fb08..45e6ee8c0 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -121,7 +121,7 @@ container:
   megafusion:
     executable:
       MegaFusion.py: "python /opt/conda/share/MegaFusion/MegaFusion.py"
-    uri: docker.io/clinicalgenomics/megafusion:66a3a80
+    uri: docker.io/clinicalgenomics/megafusion:d3feacf
   mip:
     executable:
       mip:

From 8ac8b7dca48a84e696bf37bafa8c3e2851932554 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 10 Jan 2023 15:26:43 +0100
Subject: [PATCH 09/29] remove rseqc read duplication analysis

---
 CHANGELOG.md                      |  1 +
 lib/MIP/Recipes/Analysis/Rseqc.pm | 10 ----------
 2 files changed, 1 insertion(+), 10 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 12302120f..7f76ef9cd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Updates expansionhunter variant catalog
 - Changes sv annotation overlap back to 0.8 (from 0.5) with the new tiddit update
 - New version of MegaFusion. A bug in the previous version prevented SVDB from writing the format and sample field in the vcf.
+- Remove the RSeQC read duplication analysis as it fails often.
 
 ### Tools
 
diff --git a/lib/MIP/Recipes/Analysis/Rseqc.pm b/lib/MIP/Recipes/Analysis/Rseqc.pm
index 931a6159e..6dd342ce6 100644
--- a/lib/MIP/Recipes/Analysis/Rseqc.pm
+++ b/lib/MIP/Recipes/Analysis/Rseqc.pm
@@ -292,16 +292,6 @@ sub analysis_rseqc {
     );
     say {$filehandle} $NEWLINE;
 
-    say {$filehandle} q{## Rseqc read_duplication};
-    rseqc_read_duplication(
-        {
-            filehandle           => $filehandle,
-            infile_path          => $infile_path,
-            outfiles_path_prefix => $outfile_path_prefix . $UNDERSCORE . q{read_duplication},
-        }
-    );
-    say {$filehandle} $NEWLINE;
-
     close $filehandle;
 
     if ( $recipe{mode} == 1 ) {

From d5787187fbf72a55a1035b4307ed7c6fe397ff07 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 10 Jan 2023 16:22:10 +0100
Subject: [PATCH 10/29] creating release branch

---
 CHANGELOG.md                      | 4 ++--
 documentation/Setup.md            | 2 +-
 lib/MIP/Constants.pm              | 2 +-
 templates/mip_install_config.yaml | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7f76ef9cd..95e57e8a8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,13 +3,13 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## Develop
+## [11.2.0]
 
 - Increased memory allocation for salmon and picardtools_mergersamfiles (RNA)
 - Updates expansionhunter variant catalog
 - Changes sv annotation overlap back to 0.8 (from 0.5) with the new tiddit update
 - New version of MegaFusion. A bug in the previous version prevented SVDB from writing the format and sample field in the vcf.
-- Remove the RSeQC read duplication analysis as it fails often.
+- Remove the RSeQC read duplication analysis as it often fails.
 
 ### Tools
 
diff --git a/documentation/Setup.md b/documentation/Setup.md
index cc7fbc51a..ea4a2ef0a 100644
--- a/documentation/Setup.md
+++ b/documentation/Setup.md
@@ -77,7 +77,7 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [StringTie] (version: 2.1.3b)
 - [Svdb] (version: 2.4.0)
 - [Telomerecat] (version: 3.4.0)
-- [Tiddit] (version: 2.12.1)
+- [Tiddit] (version: 3.4.0)
 - [Upd] (version: 0.1.1)
 - [Varg] (version: 1.2.0)
 - [Vcf2cytosure] (version: 0.5.1)
diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
index 8f8c7e6ad..a03ea8d72 100644
--- a/lib/MIP/Constants.pm
+++ b/lib/MIP/Constants.pm
@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{11.1.2};
+Readonly our $MIP_VERSION => q{11.2.0};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index 45e6ee8c0..cf132914d 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -125,7 +125,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:develop
+    uri: docker.io/clinicalgenomics/mip:v11.2.0
   multiqc:
     executable:
       multiqc:

From a0f96e5d9569ad11eb3dea1dc95652fa4ff32a3b Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Wed, 11 Jan 2023 11:15:08 +0100
Subject: [PATCH 11/29] longer runtime for gatk_asereadcounter

---
 CHANGELOG.md                       | 1 +
 definitions/rd_rna_parameters.yaml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 95e57e8a8..152194797 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Changes sv annotation overlap back to 0.8 (from 0.5) with the new tiddit update
 - New version of MegaFusion. A bug in the previous version prevented SVDB from writing the format and sample field in the vcf.
 - Remove the RSeQC read duplication analysis as it often fails.
+- Increased run time allocation for gatk_asereadcounter.
 
 ### Tools
 
diff --git a/definitions/rd_rna_parameters.yaml b/definitions/rd_rna_parameters.yaml
index 52d43d54c..324f76a18 100755
--- a/definitions/rd_rna_parameters.yaml
+++ b/definitions/rd_rna_parameters.yaml
@@ -146,7 +146,7 @@ recipe_time:
     dna_vcf_reformat: 1
     fastqc_ar: 1
     fusion_report: 8
-    gatk_asereadcounter: 3
+    gatk_asereadcounter: 8
     gatk_baserecalibration: 5
     gatk_haplotypecaller: 12
     gatk_splitncigarreads: 16

From 3b4ace884d11c7298be0971fb93e10a00686a146 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Mon, 23 Jan 2023 17:34:01 +0100
Subject: [PATCH 12/29] keep only trimmed rna reads longer than 40 bp

---
 CHANGELOG.md                            |  1 +
 definitions/rd_rna_parameters.yaml      |  7 +++++++
 lib/MIP/Cli/Mip/Analyse/Rd_rna.pm       |  8 ++++++++
 lib/MIP/Program/Trim_galore.pm          | 11 +++++++++++
 lib/MIP/Recipes/Analysis/Trim_galore.pm |  1 +
 t/trim_galore.t                         | 12 +++++++-----
 6 files changed, 35 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 152194797..6f2341108 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - New version of MegaFusion. A bug in the previous version prevented SVDB from writing the format and sample field in the vcf.
 - Remove the RSeQC read duplication analysis as it often fails.
 - Increased run time allocation for gatk_asereadcounter.
+- Increased the default required length for a trimmed rna read to be retained from 20 bp to 40 bp. Configurable via CLI or config.
 
 ### Tools
 
diff --git a/definitions/rd_rna_parameters.yaml b/definitions/rd_rna_parameters.yaml
index 324f76a18..508b6578c 100755
--- a/definitions/rd_rna_parameters.yaml
+++ b/definitions/rd_rna_parameters.yaml
@@ -301,6 +301,13 @@ trim_galore_ar:
   program_executables:
     - trim_galore
   type: recipe
+trim_min_length:
+  associated_recipe:
+    - trim_galore_ar
+  data_type: SCALAR
+  default: 40
+  mandatory: no
+  type: recipe_argument
 ## Salmon
 salmon_quant:
   analysis_mode: sample
diff --git a/lib/MIP/Cli/Mip/Analyse/Rd_rna.pm b/lib/MIP/Cli/Mip/Analyse/Rd_rna.pm
index 4a807e871..10aa523bf 100644
--- a/lib/MIP/Cli/Mip/Analyse/Rd_rna.pm
+++ b/lib/MIP/Cli/Mip/Analyse/Rd_rna.pm
@@ -976,6 +976,14 @@ q{Regular expression file containing the regular expression to be used for each
         )
     );
 
+    option(
+        q{trim_min_length} => (
+            documentation => q{Discard trimmed reads shorter than this},
+            is            => q{rw},
+            isa           => Int,
+        )
+    );
+
     option(
         q{vcfparser_ar} => (
             cmd_tags      => [q{Analysis recipe switch}],
diff --git a/lib/MIP/Program/Trim_galore.pm b/lib/MIP/Program/Trim_galore.pm
index 876630ef4..0476664a4 100644
--- a/lib/MIP/Program/Trim_galore.pm
+++ b/lib/MIP/Program/Trim_galore.pm
@@ -37,6 +37,7 @@ sub trim_galore {
 ##          : $filehandle             => Filehandle to write to
 ##          : $gzip_output            => Gzip output fastq file
 ##          : $infile_paths_ref       => Infile paths {REF}
+##          : $length                 => Minimum length of trimmed read to retain
 ##          : $outdir_path            => Outdirectory path
 ##          : $paired_reads           => Do paired end trimming
 ##          : $stderrfile_path        => Stderrfile path
@@ -50,6 +51,7 @@ sub trim_galore {
     my $cores;
     my $filehandle;
     my $infile_paths_ref;
+    my $length;
     my $outdir_path;
     my $paired_reads;
     my $stderrfile_path;
@@ -88,6 +90,11 @@ sub trim_galore {
             store       => \$infile_paths_ref,
             strict_type => 1,
         },
+        length => {
+            allow       => [ undef, qr/\A \d+ \z/xms ],
+            store       => \$length,
+            strict_type => 1,
+        },
         outdir_path => {
             store       => \$outdir_path,
             strict_type => 1,
@@ -137,6 +144,10 @@ sub trim_galore {
         push @commands, q{--paired};
     }
 
+    if ($length) {
+        push @commands, q{--length} . $SPACE . $length;
+    }
+
     push @commands, join $SPACE, @{$infile_paths_ref};
 
     push @commands,
diff --git a/lib/MIP/Recipes/Analysis/Trim_galore.pm b/lib/MIP/Recipes/Analysis/Trim_galore.pm
index 9cfb2bbeb..decc92cb6 100644
--- a/lib/MIP/Recipes/Analysis/Trim_galore.pm
+++ b/lib/MIP/Recipes/Analysis/Trim_galore.pm
@@ -278,6 +278,7 @@ sub analysis_trim_galore {
                 cores            => $process_core_number,
                 filehandle       => $filehandle,
                 infile_paths_ref => \@fastq_files,
+                length           => $active_parameter_href->{trim_min_length},
                 outdir_path      => $outsample_directory,
                 paired_reads     => $paired_reads,
                 stderrfile_path  => $stderrfile_path,
diff --git a/t/trim_galore.t b/t/trim_galore.t
index b2590ac79..e3adf2e64 100644
--- a/t/trim_galore.t
+++ b/t/trim_galore.t
@@ -23,16 +23,13 @@ use lib catdir( dirname($Bin), q{lib} );
 use MIP::Constants qw{ $COMMA $SPACE };
 use MIP::Test::Commands qw{ test_function };
 
-
 BEGIN {
 
     use MIP::Test::Fixtures qw{ test_import };
 
 ### Check all internal dependency modules and imports
 ## Modules with import
-    my %perl_module = (
-        q{MIP::Program::Trim_galore} => [qw{ trim_galore }],
-);
+    my %perl_module = ( q{MIP::Program::Trim_galore} => [qw{ trim_galore }], );
 
     test_import( { perl_module_href => \%perl_module, } );
 }
@@ -47,7 +44,8 @@ diag(   q{Test trim_galore from Trim_galore.pm}
       . $SPACE
       . $EXECUTABLE_NAME );
 
-Readonly my $CORES => 12;
+Readonly my $CORES      => 12;
+Readonly my $MIN_LENGTH => 30;
 
 ## Base arguments
 my @function_base_commands = qw{ trim_galore };
@@ -97,6 +95,10 @@ my %specific_argument = (
         inputs_ref      => [qw{ file_1.fastq file_2.fastq }],
         expected_output => q{file_1.fastq} . $SPACE . q{file_2.fastq},
     },
+    length => {
+        input           => $MIN_LENGTH,
+        expected_output => q{--length} . $SPACE . $MIN_LENGTH,
+    },
     outdir_path => {
         input           => catdir(qw{ output dir }),
         expected_output => q{--output_dir} . $SPACE . catdir(qw{ output dir }),

From 24ecad33135a4ee6ff92e11db608ac385b231ab7 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Thu, 2 Feb 2023 09:56:21 +0100
Subject: [PATCH 13/29] update gnomad sv database

---
 CHANGELOG.md                                    |  1 +
 lib/MIP/Recipes/Download/Gnomad.pm              |  6 +++---
 templates/mip_download_rd_dna_config_-1.0-.yaml | 14 +++++++-------
 3 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6f2341108..894504326 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Remove the RSeQC read duplication analysis as it often fails.
 - Increased run time allocation for gatk_asereadcounter.
 - Increased the default required length for a trimmed rna read to be retained from 20 bp to 40 bp. Configurable via CLI or config.
+- Fixed a bug where gnomad SV version 2.0 instead of version 2.1 was used to annotate SVs
 
 ### Tools
 
diff --git a/lib/MIP/Recipes/Download/Gnomad.pm b/lib/MIP/Recipes/Download/Gnomad.pm
index 3adda2fcc..7c9f97feb 100644
--- a/lib/MIP/Recipes/Download/Gnomad.pm
+++ b/lib/MIP/Recipes/Download/Gnomad.pm
@@ -201,7 +201,7 @@ sub download_gnomad {
             },
             method => \&_annotate,
         },
-        q{r2.1.1_sv} => {
+        q{r2.1_sv} => {
             arg_href => {
                 info_keys_ref => [qw{ INFO/AC INFO/AF INFO/POPMAX_AF }],
             },
@@ -723,7 +723,7 @@ sub _build_af_file {
             strict_type => 1,
         },
         reference_version => {
-            allow       => [qw{ r2.0.1 r2.1.1 r2.1.1_sv r3.1.1 r3.1.2 }],
+            allow       => [qw{ r2.0.1 r2.1.1 r2.1_sv r3.1.1 r3.1.2 }],
             required    => 1,
             store       => \$reference_version,
             strict_type => 1,
@@ -737,7 +737,7 @@ sub _build_af_file {
     use MIP::Program::Htslib qw{ htslib_bgzip htslib_tabix };
 
     ## Don't build file for SV:s
-    return if ( $reference_version eq q{r2.1.1_sv} );
+    return if ( $reference_version eq q{r2.1_sv} );
 
     my $outfile_no_suffix = remove_file_path_suffix(
         {
diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml
index 585795270..c8a478952 100644
--- a/templates/mip_download_rd_dna_config_-1.0-.yaml
+++ b/templates/mip_download_rd_dna_config_-1.0-.yaml
@@ -91,7 +91,7 @@ reference:
   gnomad:
     - r2.0.1
     - r2.1.1
-    - r2.1.1_sv
+    - r2.1_sv
   gnomad_chrsplit:
     - r3.1.1
     - r3.1.2
@@ -789,12 +789,12 @@ reference_feature:
         outfile: grch37_gnomad.genomes_-r2.1.1-.vcf.gz
         outfile_index: grch37_gnomad.genomes_-r2.1.1-.vcf.gz.tbi
         url_prefix: https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/genomes/
-      r2.1.1_sv:
-        file: gnomad_v2_sv.sites.vcf.gz
-        file_index: gnomad_v2_sv.sites.vcf.gz.tbi
-        outfile: grch37_gnomad.genomes_-r2.1.1_sv-.vcf.gz
-        outfile_index: grch37_gnomad.genomes_-r2.1.1_sv-.vcf.gz.tbi
-        url_prefix: https://storage.googleapis.com/gnomad-public/papers/2019-sv/
+      r2.1_sv:
+        file: gnomad_v2.1_sv.sites.vcf.gz
+        file_index: gnomad_v2.1_sv.sites.vcf.gz.tbi
+        outfile: grch37_gnomad.genomes_-r2.1_sv-.vcf.gz
+        outfile_index: grch37_gnomad.genomes_-r2.1_sv-.vcf.gz.tbi
+        url_prefix: https://storage.googleapis.com/gcp-public-data--gnomad/papers/2019-sv/gnomad_v2.1_sv.sites.vcf.gz
     grch38:
       r2.1.1:
         file: gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz

From d80aca3fc0f394fb294eca7266549c59b00c1f01 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Thu, 2 Feb 2023 10:39:21 +0100
Subject: [PATCH 14/29] fixing url

---
 templates/mip_download_rd_dna_config_-1.0-.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml
index c8a478952..9f48aea1c 100644
--- a/templates/mip_download_rd_dna_config_-1.0-.yaml
+++ b/templates/mip_download_rd_dna_config_-1.0-.yaml
@@ -794,7 +794,7 @@ reference_feature:
         file_index: gnomad_v2.1_sv.sites.vcf.gz.tbi
         outfile: grch37_gnomad.genomes_-r2.1_sv-.vcf.gz
         outfile_index: grch37_gnomad.genomes_-r2.1_sv-.vcf.gz.tbi
-        url_prefix: https://storage.googleapis.com/gcp-public-data--gnomad/papers/2019-sv/gnomad_v2.1_sv.sites.vcf.gz
+        url_prefix: https://storage.googleapis.com/gcp-public-data--gnomad/papers/2019-sv/
     grch38:
       r2.1.1:
         file: gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz

From 142f3abbf172fc1847928a632f9c94602428d68e Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Mon, 13 Feb 2023 17:34:37 +0100
Subject: [PATCH 15/29] fixing MT deletetion calculation, fixes #2016

---
 CHANGELOG.md                        | 1 +
 lib/MIP/Recipes/Analysis/Mitodel.pm | 9 ++++++---
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 894504326..9917eabcd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Increased run time allocation for gatk_asereadcounter.
 - Increased the default required length for a trimmed rna read to be retained from 20 bp to 40 bp. Configurable via CLI or config.
 - Fixed a bug where gnomad SV version 2.0 instead of version 2.1 was used to annotate SVs
+- Fixed a bug in the mitochondrial deletion recipe affecting samples with 0 intermediate discordant MT reads
 
 ### Tools
 
diff --git a/lib/MIP/Recipes/Analysis/Mitodel.pm b/lib/MIP/Recipes/Analysis/Mitodel.pm
index 0729f16f3..6f2563f40 100644
--- a/lib/MIP/Recipes/Analysis/Mitodel.pm
+++ b/lib/MIP/Recipes/Analysis/Mitodel.pm
@@ -230,14 +230,17 @@ sub analysis_mitodel {
 
     my $awk_statement =
 
+      # Set start value for intermediate discordant
+      q?BEGIN {sum=0} ?
+
       # identification of read pairs that are separated by >1.2 kb but <15 kb
-      q?($2>=1200 && $2<=15000) {sum=sum+$3}?
+      . q?($2>=1200 && $2<=15000) {sum=sum+$3} ?
 
       # identification of normal read pairs which are <1.2 kb but >15 kb
-      . q?($2<1200 || $2>15000) {sum_norm=sum_norm+$3}?
+      . q?($2<1200 || $2>15000) {sum_norm=sum_norm+$3} ?
 
       # Add end rule
-      . q?END?
+      . q?END ?
 
       # ratio of discordant to normal read pairs
       . q?{print "intermediate discordant ", sum, "normal ", sum_norm, "ratio ppk", sum*1000/(sum_norm+sum)}?;

From 6366de05fc1b372c136088e254d93921c55de399 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 21 Feb 2023 09:09:42 +0100
Subject: [PATCH 16/29] updates clinvar and loqus

---
 CHANGELOG.md                                  |  7 +-
 ...ch37_clinvar_reformated_-20230218-.vcf.gz} |  0
 ..._clinvar_reformated_-20230218-.vcf.gz.tbi} |  0
 ..._loqusdb_sv_variants_export-20230214-.vcf} |  0
 .../mip_download_rd_dna_config_-1.0-.yaml     | 84 +++++++++----------
 templates/mip_rd_dna_config.yaml              |  4 +-
 6 files changed, 50 insertions(+), 45 deletions(-)
 rename t/data/references/{grch37_clinvar_reformated_-20220829-.vcf.gz => grch37_clinvar_reformated_-20230218-.vcf.gz} (100%)
 rename t/data/references/{grch37_clinvar_reformated_-20220829-.vcf.gz.tbi => grch37_clinvar_reformated_-20230218-.vcf.gz.tbi} (100%)
 rename t/data/references/{grch37_loqusdb_sv_variants_export-20220905-.vcf => grch37_loqusdb_sv_variants_export-20230214-.vcf} (100%)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9917eabcd..8713b4e65 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,11 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Tiddit 3.3.2 -> 3.4.0
 - MegaFusion 66a3a80 -> d3feacf
 
+### Databases
+
+clinvar: 20220829 -> 20230218
+loqusdb snapshot: 20230208 -> 20230214
+
 ## [11.1.1]
 
 - Updates chromgraph to version 1.3.1
@@ -69,7 +74,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - dbnsfp: 4.1a -> 4.3a (grch38 only)
 - gnomad: r3.1.1 -> r3.1.2 (grch38 only)
 - giab: 3.3.2 -> 4.2.1
-- loqusdb dump: 20210921 -> 20220905
+- loqusdb dump: 20210921 -> c
 - nist: v3.3.2 -> v4.2.1
 - vcf2cytosure blacklist: 200520
 
diff --git a/t/data/references/grch37_clinvar_reformated_-20220829-.vcf.gz b/t/data/references/grch37_clinvar_reformated_-20230218-.vcf.gz
similarity index 100%
rename from t/data/references/grch37_clinvar_reformated_-20220829-.vcf.gz
rename to t/data/references/grch37_clinvar_reformated_-20230218-.vcf.gz
diff --git a/t/data/references/grch37_clinvar_reformated_-20220829-.vcf.gz.tbi b/t/data/references/grch37_clinvar_reformated_-20230218-.vcf.gz.tbi
similarity index 100%
rename from t/data/references/grch37_clinvar_reformated_-20220829-.vcf.gz.tbi
rename to t/data/references/grch37_clinvar_reformated_-20230218-.vcf.gz.tbi
diff --git a/t/data/references/grch37_loqusdb_sv_variants_export-20220905-.vcf b/t/data/references/grch37_loqusdb_sv_variants_export-20230214-.vcf
similarity index 100%
rename from t/data/references/grch37_loqusdb_sv_variants_export-20220905-.vcf
rename to t/data/references/grch37_loqusdb_sv_variants_export-20230214-.vcf
diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml
index 9f48aea1c..5982bdc46 100644
--- a/templates/mip_download_rd_dna_config_-1.0-.yaml
+++ b/templates/mip_download_rd_dna_config_-1.0-.yaml
@@ -26,8 +26,8 @@ reference:
   chromograph_cytoband:
     - v1.0
   clinvar:
-    - 20211010
     - 20220829
+    - 20230218
   dbnsfp:
     - 3.5a
     - 4.1a
@@ -111,8 +111,8 @@ reference:
     - gold_standard_indels
   rank_model:
     - v0.2
-    - v1.33
     - v1.34
+    - v1.35
   reduced_penetrance:
     - 2017
   scout_exons:
@@ -124,8 +124,8 @@ reference:
     - v1.4
   svrank_model:
     - v0.1
-    - v1.8
     - v1.9
+    - v1.10
   vcf2cytosure_blacklist_regions:
     - 1.0
     - 200520
@@ -323,15 +323,6 @@ reference_feature:
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/region/
   clinvar:
     grch37:
-      20211010:
-        file: clinvar_20211010.vcf.gz
-        file_check: clinvar_20211010.vcf.gz.md5
-        file_index: clinvar_20211010.vcf.gz.tbi
-        outfile: grch37_clinvar_-20211010-.vcf.gz
-        outfile_check: grch37_clinvar_-20211010-.vcf.gz.md5
-        outfile_index: grch37_clinvar_-20211010-.vcf.gz.tbi
-        outfile_check_method: md5sum
-        url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
       20220829:
         file: clinvar_20220829.vcf.gz
         file_check: clinvar_20220829.vcf.gz.md5
@@ -341,16 +332,16 @@ reference_feature:
         outfile_index: grch37_clinvar_-20220829-.vcf.gz.tbi
         outfile_check_method: md5sum
         url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
-    grch38:
-      20211010:
-        file: clinvar_20211010.vcf.gz
-        file_check: clinvar_20211010.vcf.gz.md5
-        file_index: clinvar_20211010.vcf.gz.tbi
-        outfile: grch38_clinvar_-20211010-.vcf.gz
-        outfile_check: grch38_clinvar_-20211010-.vcf.gz.md5
-        outfile_index: grch38_clinvar_-20211010-.vcf.gz.tbi
+      20230218:
+        file: clinvar_20230218.vcf.gz
+        file_check: clinvar_20230218.vcf.gz.md5
+        file_index: clinvar_20230218.vcf.gz.tbi
+        outfile: grch37_clinvar_-20230218-.vcf.gz
+        outfile_check: grch37_clinvar_-20230218-.vcf.gz.md5
+        outfile_index: grch37_clinvar_-20230218-.vcf.gz.tbi
         outfile_check_method: md5sum
-        url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
+        url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
+    grch38:
       20220829:
         file: clinvar_20220829.vcf.gz
         file_check: clinvar_20220829.vcf.gz.md5
@@ -360,6 +351,15 @@ reference_feature:
         outfile_index: grch38_clinvar_-20220829-.vcf.gz.tbi
         outfile_check_method: md5sum
         url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
+      20230218:
+        file: clinvar_20230218.vcf.gz
+        file_check: clinvar_20230218.vcf.gz.md5
+        file_index: clinvar_20230218.vcf.gz.tbi
+        outfile: grch38_clinvar_-20230218-.vcf.gz
+        outfile_check: grch38_clinvar_-20230218-.vcf.gz.md5
+        outfile_index: grch38_clinvar_-20230218-.vcf.gz.tbi
+        outfile_check_method: md5sum
+        url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
   dbnsfp:
     grch37:
       3.5a:
@@ -900,13 +900,6 @@ reference_feature:
         url_prefix: https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/
   rank_model:
     grch37:
-      v1.33:
-        file: rank_model_-v1.33-.ini
-        file_check: rank_model_-v1.33-.ini.md5
-        outfile: rank_model_-v1.33-.ini
-        outfile_check: rank_model_-v1.33-.ini.md5
-        outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
       v1.34:
         file: rank_model_-v1.34-.ini
         file_check: rank_model_-v1.34-.ini.md5
@@ -914,6 +907,13 @@ reference_feature:
         outfile_check: rank_model_-v1.34-.ini.md5
         outfile_check_method: md5sum
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
+      v1.35:
+        file: rank_model_-v1.35-.ini
+        file_check: rank_model_-v1.35-.ini.md5
+        outfile: rank_model_-v1.35-.ini
+        outfile_check: rank_model_-v1.35-.ini.md5
+        outfile_check_method: md5sum
+        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
     grch38:
       v0.2:
         file: grch38_rank_model_-v0.2-.ini
@@ -971,13 +971,6 @@ reference_feature:
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
   svrank_model:
     grch37:
-      v1.8:
-        file: svrank_model_-v1.8-.ini
-        file_check: svrank_model_-v1.8-.ini.md5
-        outfile: svrank_model_-v1.8-.ini
-        outfile_check: svrank_model_-v1.8-.ini.md5
-        outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
       v1.9:
         file: svrank_model_-v1.9-.ini
         file_check: svrank_model_-v1.9-.ini.md5
@@ -985,6 +978,13 @@ reference_feature:
         outfile_check: svrank_model_-v1.9-.ini.md5
         outfile_check_method: md5sum
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
+      v1.10:
+        file: svrank_model_-v1.10-.ini
+        file_check: svrank_model_-v1.10-.ini.md5
+        outfile: svrank_model_-v1.10-.ini
+        outfile_check: svrank_model_-v1.10-.ini.md5
+        outfile_check_method: md5sum
+        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
     grch38:
       v0.1:
         file: grch38_sv_rank_model_-v0.1-.ini
@@ -1010,13 +1010,6 @@ reference_feature:
         url_prefix: https://www.encodeproject.org/files/ENCFF356LFX/@@download/
   vcfanno_config:
     grch37:
-      v1.17:
-        file: grch37_vcfanno_config_-v1.17-.toml
-        file_check: grch37_vcfanno_config_-v1.17-.toml.md5
-        outfile: grch37_vcfanno_config_-v1.17-.toml
-        outfile_check: grch37_vcfanno_config_-v1.17-.toml.md5
-        outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
       v1.18:
         file: grch37_vcfanno_config_-v1.18-.toml
         file_check: grch37_vcfanno_config_-v1.18-.toml.md5
@@ -1024,6 +1017,13 @@ reference_feature:
         outfile_check: grch37_vcfanno_config_-v1.18-.toml.md5
         outfile_check_method: md5sum
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
+      v1.19:
+        file: grch37_vcfanno_config_-v1.19-.toml
+        file_check: grch37_vcfanno_config_-v1.19-.toml.md5
+        outfile: grch37_vcfanno_config_-v1.19-.toml
+        outfile_check: grch37_vcfanno_config_-v1.19-.toml.md5
+        outfile_check_method: md5sum
+        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
     grch38:
       v0.2:
         file: grch38_vcfanno_config_-v0.2-.toml
diff --git a/templates/mip_rd_dna_config.yaml b/templates/mip_rd_dna_config.yaml
index 988a8d8ae..71ab1bb07 100755
--- a/templates/mip_rd_dna_config.yaml
+++ b/templates/mip_rd_dna_config.yaml
@@ -32,7 +32,7 @@ sv_svdb_query_db_files:
   # FORMAT: filename|OUT_FREQUENCY_INFO_KEY|OUT_ALLELE_COUNT_INFO_KEY|IN_FREQUENCY_INFO_KEY|IN_ALLELE_COUNT_INFO_KEY|USE_IN_FREQUENCY_FILTER
   grch37_clinvar_sv_pathogenic_-20221004-.bedpe: clinvar_pathogenic|Occ|Frq
   grch37_gnomad_reformated_-r2.1.1_sv-.vcf.gz: gnomad_sv|AF|AC|AF|AC|1
-  grch37_loqusdb_sv_variants_export-20220905-.vcf: clinical_genomics_loqus|Frq|Obs|Frq|Obs|1
+  grch37_loqusdb_sv_variants_export-20230214-.vcf: clinical_genomics_loqus|Frq|Obs|Frq|Obs|1
   grch37_mip_sv_svdb_export_-2018-10-09-.vcf: clinical_genomics_mip|AF|OCC|FRQ|OCC|1
   grch37_svdb_query_decipher_-v1.0.0-.vcf: decipher|AF|OCC|FRQ|OCC
   grch37_svdb_query_clingen_cgh_benign_-v1.0.0-.vcf: clingen_cgh_benign
@@ -76,7 +76,7 @@ vep_custom_annotation:
     force_report_coordinates: 0
     key: CLINVAR
     file_type: vcf
-    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20220829-.vcf.gz
+    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20230218-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
 vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/
 vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins

From bdd61c5cd27fcc3d01c70c1a9a919dbcac83761a Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 21 Feb 2023 09:45:35 +0100
Subject: [PATCH 17/29] fixing test files

---
 templates/mip_dragen_rd_dna_config.yaml    | 2 +-
 templates/mip_rd_dna_panel_config.yaml     | 2 +-
 templates/mip_rd_dna_vcf_rerun_config.yaml | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/templates/mip_dragen_rd_dna_config.yaml b/templates/mip_dragen_rd_dna_config.yaml
index 32338a0b7..812a051a7 100644
--- a/templates/mip_dragen_rd_dna_config.yaml
+++ b/templates/mip_dragen_rd_dna_config.yaml
@@ -68,7 +68,7 @@ vep_custom_annotation:
     force_report_coordinates: 0
     key: CLINVAR
     file_type: vcf
-    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20220829-.vcf.gz
+    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20230218-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
 vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/
 vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins
diff --git a/templates/mip_rd_dna_panel_config.yaml b/templates/mip_rd_dna_panel_config.yaml
index 4c8e9bc72..7535930ae 100755
--- a/templates/mip_rd_dna_panel_config.yaml
+++ b/templates/mip_rd_dna_panel_config.yaml
@@ -49,7 +49,7 @@ vep_custom_annotation:
     force_report_coordinates: 0
     key: CLINVAR
     file_type: vcf
-    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20220829-.vcf.gz
+    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20230218-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
 vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/
 vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins
diff --git a/templates/mip_rd_dna_vcf_rerun_config.yaml b/templates/mip_rd_dna_vcf_rerun_config.yaml
index 600579059..2cdeb228b 100644
--- a/templates/mip_rd_dna_vcf_rerun_config.yaml
+++ b/templates/mip_rd_dna_vcf_rerun_config.yaml
@@ -28,7 +28,7 @@ sv_rank_model_file: svrank_model_-v1.9-.ini
 # FORMAT: filename|OUT_FREQUENCY_INFO_KEY|OUT_ALLELE_COUNT_INFO_KEY|IN_FREQUENCY_INFO_KEY|IN_ALLELE_COUNT_INFO_KEY|USE_IN_FREQUENCY_FILTER
 sv_svdb_query_db_files:
   grch37_gnomad_reformated_-r2.1.1_sv-.vcf.gz: gnomad_sv|AF|AC|AF|AC|1
-  grch37_loqusdb_sv_variants_export-20220905-.vcf: clinical_genomics_loqus|Frq|Obs|Frq|Obs
+  grch37_loqusdb_sv_variants_export-20230214-.vcf: clinical_genomics_loqus|Frq|Obs|Frq|Obs
   grch37_mip_sv_svdb_export_-2018-10-09-.vcf: clinical_genomics_mip|AF|OCC|FRQ|OCC|1
   grch37_svdb_query_decipher_-v1.0.0-.vcf: decipher|AF|OCC|FRQ|OCC
   grch37_svdb_query_clingen_cgh_benign_-v1.0.0-.vcf: clingen_cgh_benign
@@ -70,7 +70,7 @@ vep_custom_annotation:
     force_report_coordinates: 0
     key: CLINVAR
     file_type: vcf
-    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20220829-.vcf.gz
+    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20230218-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
 vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/
 vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins

From a5c5b3cc8dffa586c05b7e73b1f41c6677d41cfe Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 21 Feb 2023 16:24:11 +0100
Subject: [PATCH 18/29] updating hmtnote dump

---
 CHANGELOG.md                      | 1 +
 containers/hmtnote/Dockerfile     | 6 +++---
 templates/mip_install_config.yaml | 2 +-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8713b4e65..9388458fd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 clinvar: 20220829 -> 20230218
 loqusdb snapshot: 20230208 -> 20230214
+hmtvar: oct2022
 
 ## [11.1.1]
 
diff --git a/containers/hmtnote/Dockerfile b/containers/hmtnote/Dockerfile
index ebade96d7..1ac78820c 100644
--- a/containers/hmtnote/Dockerfile
+++ b/containers/hmtnote/Dockerfile
@@ -5,15 +5,15 @@ FROM clinicalgenomics/mip_base:2.1
 ################## METADATA ######################
 
 LABEL base-image="clinicalgenomics/mip_base:2.1"
-LABEL version="1"
+LABEL version="2"
 LABEL software="HmtNote"
 LABEL software.version="0.7.2"
-LABEL extra.binaries="HmtNote"
+LABEL extra.binaries="HmtNote, hmtvar_oct2022"
 LABEL maintainer="Clinical-Genomics/MIP"
 
 ## Conda env installation + clean up
 RUN conda install pip python=3.7 && \
-    /opt/conda/bin/conda clean -tipsy
+    /opt/conda/bin/conda clean -ya
 
 # Install HmtNote
 RUN pip install --no-cache-dir hmtnote==0.7.2 && \
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index cf132914d..86abf7cbe 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -105,7 +105,7 @@ container:
   hmtnote:
     executable:
       hmtnote:
-    uri: docker.io/clinicalgenomics/hmtnote:0.7.2
+    uri: docker.io/clinicalgenomics/hmtnote:0.7.2-oct2022
   htslib:
     executable:
       bcftools:

From 22b7abd787dd3f7e79a1a25fae1800cc31b40121 Mon Sep 17 00:00:00 2001
From: Emil Bertilsson <emil.bertilsson@hasta.scilifelab.se>
Date: Thu, 2 Mar 2023 13:38:35 +0100
Subject: [PATCH 19/29] Adds index path to Gens deliverables

---
 lib/MIP/Recipes/Analysis/Gens_generatedata.pm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/MIP/Recipes/Analysis/Gens_generatedata.pm b/lib/MIP/Recipes/Analysis/Gens_generatedata.pm
index 892718190..628578b63 100644
--- a/lib/MIP/Recipes/Analysis/Gens_generatedata.pm
+++ b/lib/MIP/Recipes/Analysis/Gens_generatedata.pm
@@ -253,6 +253,7 @@ sub analysis_gens_generatedata {
                     format           => q{bed},
                     id               => $sample_id,
                     path             => $outfile_path{$file_tag},
+                    path_index       => $outfile_path{$file_tag} . q{.tbi},
                     recipe_name      => $recipe_name,
                     sample_info_href => $sample_info_href,
                     tag              => $file_tag,

From e001559619262c8eb593f73258b31824b21c4fab Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 21 Mar 2023 12:01:47 +0100
Subject: [PATCH 20/29] updating programs

---
 CHANGELOG.md                         | 13 +++++++++++--
 containers/fastqc/Dockerfile         | 10 ++++------
 containers/gffcompare/Dockerfile     | 19 -------------------
 containers/htslib/Dockerfile         |  6 +++---
 lib/MIP/Recipes/Analysis/Star_aln.pm | 18 ++----------------
 templates/mip_install_config.yaml    | 26 +++++++++++++-------------
 6 files changed, 33 insertions(+), 59 deletions(-)
 delete mode 100644 containers/gffcompare/Dockerfile

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 21f1a63be..41ffa7205 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,12 +13,21 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Increased run time allocation for gatk_asereadcounter.
 - Increased the default required length for a trimmed rna read to be retained from 20 bp to 40 bp. Configurable via CLI or config.
 - Fixed a bug where gnomad SV version 2.0 instead of version 2.1 was used to annotate SVs
+- One-pass instead of two-pass mapping with STAR-Fusion, as recommended for STAR-Fusion 1.12
 
 ### Tools
 
-- Tiddit 3.3.2 -> 3.4.0
+- Arriba 2.3.0 -> 2.4.0
+- DeepVariant 1.4.0 -> 1.5.0
+- FastQC: 0.11.9 -> 0.12.1
+- GATK: 4.2.6.1 -> 4.4.0.0
+- Gffcompare 0.11.2 -> 0.12.6
+- Htslib 1.15.1 -> 1.16
 - MegaFusion 66a3a80 -> d3feacf
-
+- Picard 2.27.2 -> 2.27.5
+- STAR-Fusion 1.11.0 -> 1.12.0
+- SVDB: 2.7.0 -> 2.8.1
+- Tiddit 3.3.2 -> 3.4.0
 ### Databases
 
 clinvar: 20220829 -> 20230218
diff --git a/containers/fastqc/Dockerfile b/containers/fastqc/Dockerfile
index 04a801a2f..8c146a3a2 100644
--- a/containers/fastqc/Dockerfile
+++ b/containers/fastqc/Dockerfile
@@ -5,15 +5,13 @@ FROM clinicalgenomics/mip_base:2.1
 ################## METADATA ######################
 
 LABEL base_image="clinicalgenomics/mip_base:2.1"
-LABEL version="2"
+LABEL version="3"
 LABEL software="fastqc"
-LABEL software.version="0.11.9"
+LABEL software.version="0.12.1"
 LABEL extra.binaries="fastqc"
 LABEL maintainer="Clinical-Genomics/MIP"
 
-RUN conda install fastqc=0.11.9=0
-
-## Clean up after conda
-RUN /opt/conda/bin/conda clean -tipsy
+RUN conda install fastqc=0.12.1 && \
+    /opt/conda/bin/conda clean -ya
 
 WORKDIR /data/
diff --git a/containers/gffcompare/Dockerfile b/containers/gffcompare/Dockerfile
deleted file mode 100644
index 617cfdc74..000000000
--- a/containers/gffcompare/Dockerfile
+++ /dev/null
@@ -1,19 +0,0 @@
-################## BASE IMAGE ######################
-
-FROM clinicalgenomics/mip_base:2.1
-
-################## METADATA ######################
-
-LABEL base_image="clinicalgenomics/mip_base:2.1"
-LABEL version="1"
-LABEL software="gffcompare"
-LABEL software.version="0.11.2"
-LABEL extra.binaries="gffcompare"
-LABEL maintainer="Clinical-Genomics/MIP"
-
-RUN conda install --yes gffcompare=0.11.2
-
-## Clean up after conda
-RUN /opt/conda/bin/conda clean -ay
-
-WORKDIR /data/
diff --git a/containers/htslib/Dockerfile b/containers/htslib/Dockerfile
index 870a76eae..e46b9254f 100644
--- a/containers/htslib/Dockerfile
+++ b/containers/htslib/Dockerfile
@@ -5,13 +5,13 @@ FROM clinicalgenomics/mip_base:2.1
 ################## METADATA ######################
 
 LABEL base-image="clinicalgenomics/mip_base:2.1"
-LABEL version="7"
+LABEL version="8"
 LABEL software="htslib"
-LABEL software.version="1.15.1"
+LABEL software.version="1.16"
 LABEL extra.binaries="bcftools, bgzip, samtools, tabix"
 LABEL maintainer="Clinical-Genomics/MIP"
 
-RUN conda install bcftools=1.15.1 htslib=1.15.1 samtools=1.15.1 && \
+RUN conda install bcftools=1.16 htslib=1.16 samtools=1.16.1 && \
     /opt/conda/bin/conda clean -ya
 
 WORKDIR /data/
diff --git a/lib/MIP/Recipes/Analysis/Star_aln.pm b/lib/MIP/Recipes/Analysis/Star_aln.pm
index 41655cb10..e693ed838 100644
--- a/lib/MIP/Recipes/Analysis/Star_aln.pm
+++ b/lib/MIP/Recipes/Analysis/Star_aln.pm
@@ -1037,8 +1037,9 @@ sub analysis_star_fusion_aln {
             outfile_name_prefix                    => $outfile_path_prefix . $DOT,
             pe_overlap_mmp                         => $PE_OVERLAP_MMP,
             pe_overlap_nbases_min                  => $PE_OVERLAP_NBASES_MIN,
+            quant_mode                             => q{GeneCounts},
             thread_number                          => $recipe{core_number},
-            two_pass_mode                          => q{Basic},
+            two_pass_mode                          => q{None},
         },
     );
     say {$filehandle} $NEWLINE;
@@ -1053,21 +1054,6 @@ sub analysis_star_fusion_aln {
     );
     say {$filehandle} $NEWLINE;
 
-    ## Remove intermediary files
-  FILE_TAG:
-    foreach my $file_tag (qw{ _STARgenome _STARpass1 }) {
-
-        gnu_rm(
-            {
-                filehandle  => $filehandle,
-                force       => 1,
-                infile_path => $outfile_path_prefix . $DOT . $file_tag,
-                recursive   => 1,
-            }
-        );
-        print {$filehandle} $NEWLINE;
-    }
-
     ## Close filehandle
     close $filehandle or $log->logcroak(q{Could not close filehandle});
 
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index 86abf7cbe..7d1c624b3 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -2,9 +2,9 @@
 container:
   arriba:
     executable:
-      arriba: /arriba_v2.3.0/arriba
-      draw_fusions.R: /arriba_v2.3.0/draw_fusions.R
-    uri: docker.io/uhrigs/arriba:2.3.0
+      arriba: /arriba_v2.4.0/arriba
+      draw_fusions.R: /arriba_v2.4.0/draw_fusions.R
+    uri: docker.io/uhrigs/arriba:2.4.0
   bedtools:
     executable:
       bedtools:
@@ -60,12 +60,12 @@ container:
       call_variants: /opt/deepvariant/bin/call_variants
       postprocess_variants: /opt/deepvariant/bin/postprocess_variants
     gpu_support: 0
-    uri: docker.io/google/deepvariant:1.4.0
+    uri: docker.io/google/deepvariant:1.5.0
   deeptrio:
     executable:
       run_deeptrio: /opt/deepvariant/bin/deeptrio/run_deeptrio
     gpu_support: 0
-    uri: docker.io/google/deepvariant:deeptrio-1.4.0
+    uri: docker.io/google/deepvariant:deeptrio-1.5.0
   delly:
     executable:
       delly:
@@ -77,7 +77,7 @@ container:
   fastqc:
     executable:
       fastqc:
-    uri: docker.io/clinicalgenomics/fastqc:0.11.9
+    uri: docker.io/clinicalgenomics/fastqc:0.12.1
   gatk:
     executable:
       gatk3: "no_executable_in_image"
@@ -85,7 +85,7 @@ container:
   gatk4:
     executable:
       gatk:
-    uri: docker.io/broadinstitute/gatk:4.2.6.1
+    uri: docker.io/broadinstitute/gatk:4.4.0.0
   genmod:
     executable:
       genmod:
@@ -97,7 +97,7 @@ container:
   gffcompare:
     executable:
       gffcompare:
-    uri: docker.io/clinicalgenomics/gffcompare:0.11.2
+    uri: quay.io/biocontainers/gffcompare:0.12.6--h9f5acd7_0
   glnexus:
     executable:
       glnexus_cli:
@@ -112,7 +112,7 @@ container:
       bgzip:
       samtools:
       tabix:
-    uri: docker.io/clinicalgenomics/htslib:1.15.1
+    uri: docker.io/clinicalgenomics/htslib:1.16
   manta:
     executable:
       configManta.py:
@@ -129,7 +129,7 @@ container:
   multiqc:
     executable:
       multiqc:
-    uri: docker.io/ewels/multiqc:v1.12
+    uri: docker.io/ewels/multiqc:v1.14
   perl:
     executable:
       perl:
@@ -145,7 +145,7 @@ container:
   picard:
     executable:
       picard: "no_executable_in_image"
-    uri: docker.io/broadinstitute/picard:2.27.2
+    uri: docker.io/broadinstitute/picard:2.27.5
   plink:
     executable:
       plink2:
@@ -201,7 +201,7 @@ container:
       remove_long_intron_readthru_transcripts.pl: /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/util/remove_long_intron_readthru_transcripts.pl
       restrict_genome_to_chr_entries.pl: /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/util/restrict_genome_to_chr_entries.pl
       STAR-Fusion: /usr/local/src/STAR-Fusion/STAR-Fusion
-    uri: docker.io/trinityctat/starfusion:1.11.0
+    uri: docker.io/trinityctat/starfusion:1.12.0
   stranger:
     executable:
       stranger:
@@ -213,7 +213,7 @@ container:
   svdb:
     executable:
       svdb:
-    uri: quay.io/biocontainers/svdb:2.7.0--py39h5371cbf_0
+    uri: quay.io/biocontainers/svdb:2.8.1--py310h79ef01b_0
   telomerecat:
     executable:
       telomerecat:

From 9bc1080101677bd6fb89059819299c1efddbb8af Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Mon, 8 May 2023 16:40:20 +0200
Subject: [PATCH 21/29] updates svdb and tiddit to latest versions

---
 CHANGELOG.md                      | 5 +++--
 templates/mip_install_config.yaml | 4 ++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e64fb4623..b71653912 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Develop]
 
+- Update Tiddit to improve SV positioning
 - Increased memory allocation for salmon and picardtools_mergersamfiles (RNA)
 - Changes sv annotation overlap back to 0.8 (from 0.5) with the new tiddit update
 - New version of MegaFusion. A bug in the previous version prevented SVDB from writing the format and sample field in the vcf.
@@ -25,8 +26,8 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - MegaFusion 66a3a80 -> d3feacf
 - Picard 2.27.2 -> 2.27.5
 - STAR-Fusion 1.11.0 -> 1.12.0
-- SVDB: 2.7.0 -> 2.8.1
-- Tiddit 3.3.2 -> 3.4.0
+- SVDB: 2.7.0 -> 2.8.2
+- Tiddit 3.3.2 -> 3.6.0
 
 ### Databases
 
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index c88a245a7..956af52b0 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -217,7 +217,7 @@ container:
   svdb:
     executable:
       svdb:
-    uri: quay.io/biocontainers/svdb:2.8.1--py310h79ef01b_0
+    uri: docker.io/clinicalgenomics/svdb:2.8.2
   telomerecat:
     executable:
       telomerecat:
@@ -225,7 +225,7 @@ container:
   tiddit:
     executable:
       tiddit:
-    uri: quay.io/biocontainers/tiddit:3.4.0--py310hc2b7f4b_0
+    uri: quay.io/biocontainers/tiddit:3.6.0--py310hc2b7f4b_0
   trim-galore:
     executable:
       trim_galore:

From 663ee28fa02251853aa2d2bf2c3c11d4e2257c0f Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Mon, 8 May 2023 17:19:05 +0200
Subject: [PATCH 22/29] modifying sv overlap requirements

---
 CHANGELOG.md                                          |  3 ++-
 definitions/rd_dna_parameters.yaml                    |  8 +++++++-
 documentation/Setup.md                                |  4 ++--
 lib/MIP/Cli/Mip/Analyse/Rd_dna.pm                     | 10 +++++++++-
 lib/MIP/Recipes/Analysis/Sv_combinevariantcallsets.pm | 11 +++--------
 5 files changed, 23 insertions(+), 13 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b71653912..677e163ab 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,9 +5,10 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Develop]
 
+- Set overlap requirement for merging two SVs to 0.6
+- Set overlap requirement for SV annotation to 0.6, up from 0.5
 - Update Tiddit to improve SV positioning
 - Increased memory allocation for salmon and picardtools_mergersamfiles (RNA)
-- Changes sv annotation overlap back to 0.8 (from 0.5) with the new tiddit update
 - New version of MegaFusion. A bug in the previous version prevented SVDB from writing the format and sample field in the vcf.
 - Remove the RSeQC read duplication analysis as it often fails.
 - Increased run time allocation for gatk_asereadcounter.
diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
index 6284ac13b..9308edbb5 100755
--- a/definitions/rd_dna_parameters.yaml
+++ b/definitions/rd_dna_parameters.yaml
@@ -959,6 +959,12 @@ sv_svdb_merge_prioritize:
   data_type: SCALAR
   default: tiddit,cnvnator,manta
   type: recipe_argument
+sv_svdb_merge_overlap:
+  associated_recipe:
+    - sv_combinevariantcallsets
+  data_type: SCALAR
+  default: 0.8
+  type: recipe_argument
 sv_decompose:
   associated_recipe:
     - sv_combinevariantcallsets
@@ -1015,7 +1021,7 @@ sv_svdb_query_overlap:
   associated_recipe:
     - sv_annotate
   data_type: SCALAR
-  default: 0.8
+  default: 0.6
   type: recipe_argument
 sv_vcfanno_config:
   associated_recipe:
diff --git a/documentation/Setup.md b/documentation/Setup.md
index a1a43c20c..edb0e7ac9 100644
--- a/documentation/Setup.md
+++ b/documentation/Setup.md
@@ -76,9 +76,9 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [STAR] (version: 2.7.8a)
 - [Stranger] (version: 0.8.0)
 - [StringTie] (version: 2.1.3b)
-- [Svdb] (version: 2.4.0)
+- [Svdb] (version: 2.8.2)
 - [Telomerecat] (version: 3.4.0)
-- [Tiddit] (version: 3.4.0)
+- [Tiddit] (version: 3.6.0)
 - [Upd] (version: 0.1.1)
 - [Varg] (version: 1.2.0)
 - [Vcf2cytosure] (version: 0.5.1)
diff --git a/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm b/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm
index 88d3cfafd..ae5f3fe42 100644
--- a/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm
+++ b/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm
@@ -827,6 +827,14 @@ q{Default: grch37_dbsnp_-138-.vcf, grch37_1000g_indels_-phase1-.vcf, grch37_mill
         )
     );
 
+    option(
+        q{sv_svdb_merge_overlap} => (
+            documentation => q{Required overlap to merge two structural variants},
+            is            => q{rw},
+            isa           => Num,
+        )
+    );
+
     option(
         q{sv_svdb_merge_prioritize} => (
             documentation => q{Prioritization order of structural variant callers},
@@ -897,7 +905,7 @@ q{Default: grch37_dbsnp_-138-.vcf, grch37_1000g_indels_-phase1-.vcf, grch37_mill
         q{sv_svdb_query_overlap} => (
             documentation => q{Database file(s) for annotation},
             is            => q{rw},
-            isa           => Str,
+            isa           => Num,
         )
     );
 
diff --git a/lib/MIP/Recipes/Analysis/Sv_combinevariantcallsets.pm b/lib/MIP/Recipes/Analysis/Sv_combinevariantcallsets.pm
index 4fd17f8ee..7d6d88a43 100644
--- a/lib/MIP/Recipes/Analysis/Sv_combinevariantcallsets.pm
+++ b/lib/MIP/Recipes/Analysis/Sv_combinevariantcallsets.pm
@@ -280,8 +280,9 @@ sub analysis_sv_combinevariantcallsets {
         {
             filehandle       => $filehandle,
             infile_paths_ref => \@svdb_infile_paths,
-            priority         => $active_parameter_href->{sv_svdb_merge_prioritize},
+            overlap          => $active_parameter_href->{sv_svdb_merge_overlap},
             pass_only        => 1,
+            priority         => $active_parameter_href->{sv_svdb_merge_prioritize},
             same_order       => 1,
             stdoutfile_path  => $outfile_path,
         }
@@ -425,13 +426,7 @@ sub _add_to_parallel_chain {
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
     ## If element is not part of array
-    if (
-        not any {
-            $_ eq $structural_variant_caller_chain
-        }
-        @{$parallel_chains_ref}
-      )
-    {
+    if ( not any { $_ eq $structural_variant_caller_chain } @{$parallel_chains_ref} ) {
         push @{$parallel_chains_ref}, $structural_variant_caller_chain;
     }
     return;

From a7bb25c197707c723d6dd44aed1bb55870244157 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Mon, 8 May 2023 17:29:04 +0200
Subject: [PATCH 23/29] updating mip version tag to reflect develop

---
 lib/MIP/Constants.pm              | 2 +-
 templates/mip_install_config.yaml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
index 8b425d3d9..d6434afa0 100644
--- a/lib/MIP/Constants.pm
+++ b/lib/MIP/Constants.pm
@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{11.2.1};
+Readonly our $MIP_VERSION => q{12.0.0-develop};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index 956af52b0..12607db94 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -125,7 +125,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:v11.2.1
+    uri: docker.io/clinicalgenomics/mip:develop
   multiqc:
     executable:
       multiqc:

From 5329ed0c01bda8eb43ceb73afaff8ea732f4ba5f Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Fri, 12 May 2023 09:02:22 +0200
Subject: [PATCH 24/29] fixing changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c6c44ddaa..efe4af122 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Develop]
 
-- Set overlap requirement for merging two SVs to 0.6
+- Set overlap requirement for merging two SVs to 0.8, down from the 0.95 default
 - Set overlap requirement for SV annotation to 0.6, up from 0.5
 - Update Tiddit to improve SV positioning
 - Increased memory allocation for salmon and picardtools_mergersamfiles (RNA)

From c1ef637af567c37f322a96f492dc4cc3790c8a88 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Fri, 12 May 2023 10:19:22 +0200
Subject: [PATCH 25/29] increasing max retroseq run time to 15 h

---
 CHANGELOG.md                       | 1 +
 definitions/rd_dna_parameters.yaml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index efe4af122..79b12a9de 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Increased the default required length for a trimmed rna read to be retained from 20 bp to 40 bp. Configurable via CLI or config.
 - Fixed a bug where gnomad SV version 2.0 instead of version 2.1 was used to annotate SVs
 - One-pass instead of two-pass mapping with STAR-Fusion, as recommended for STAR-Fusion 1.12
+- Bump max run time for retroseq to 15 hours.
 
 ### Tools
 
diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
index 9308edbb5..8dcd61723 100755
--- a/definitions/rd_dna_parameters.yaml
+++ b/definitions/rd_dna_parameters.yaml
@@ -377,7 +377,7 @@ recipe_time:
     prepareforvariantannotationblock: 5
     qccollect_ar: 1
     rankvariant: 10
-    retroseq: 5
+    retroseq: 15
     rhocall_ar: 5
     rhocall_viz: 1
     rtg_vcfeval: 1

From 6bc34e09a3c8e4afb1e77e2749ad4a1e3229430b Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Fri, 12 May 2023 15:02:34 +0200
Subject: [PATCH 26/29] uppdates clinvar references

---
 CHANGELOG.md                                  |  4 +--
 .../mip_download_rd_dna_config_-1.0-.yaml     | 30 +++++++++----------
 2 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 79b12a9de..8a7b5c892 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -33,8 +33,8 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ### Databases
 
-clinvar: 20220829 -> 20230218
-loqusdb snapshot: 20230208 -> 20230214
+clinvar: 20220829 -> 20230508
+loqusdb snapshot: 20230208 -> 20230512
 hmtvar: oct2022
 
 ## [11.2.2]
diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml
index 5982bdc46..9adeef3d6 100644
--- a/templates/mip_download_rd_dna_config_-1.0-.yaml
+++ b/templates/mip_download_rd_dna_config_-1.0-.yaml
@@ -27,7 +27,7 @@ reference:
     - v1.0
   clinvar:
     - 20220829
-    - 20230218
+    - 20230508
   dbnsfp:
     - 3.5a
     - 4.1a
@@ -332,13 +332,13 @@ reference_feature:
         outfile_index: grch37_clinvar_-20220829-.vcf.gz.tbi
         outfile_check_method: md5sum
         url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
-      20230218:
-        file: clinvar_20230218.vcf.gz
-        file_check: clinvar_20230218.vcf.gz.md5
-        file_index: clinvar_20230218.vcf.gz.tbi
-        outfile: grch37_clinvar_-20230218-.vcf.gz
-        outfile_check: grch37_clinvar_-20230218-.vcf.gz.md5
-        outfile_index: grch37_clinvar_-20230218-.vcf.gz.tbi
+      20230508:
+        file: clinvar_20230508.vcf.gz
+        file_check: clinvar_20230508.vcf.gz.md5
+        file_index: clinvar_20230508.vcf.gz.tbi
+        outfile: grch37_clinvar_-20230508-.vcf.gz
+        outfile_check: grch37_clinvar_-20230508-.vcf.gz.md5
+        outfile_index: grch37_clinvar_-20230508-.vcf.gz.tbi
         outfile_check_method: md5sum
         url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
     grch38:
@@ -351,13 +351,13 @@ reference_feature:
         outfile_index: grch38_clinvar_-20220829-.vcf.gz.tbi
         outfile_check_method: md5sum
         url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
-      20230218:
-        file: clinvar_20230218.vcf.gz
-        file_check: clinvar_20230218.vcf.gz.md5
-        file_index: clinvar_20230218.vcf.gz.tbi
-        outfile: grch38_clinvar_-20230218-.vcf.gz
-        outfile_check: grch38_clinvar_-20230218-.vcf.gz.md5
-        outfile_index: grch38_clinvar_-20230218-.vcf.gz.tbi
+      20230508:
+        file: clinvar_20230508.vcf.gz
+        file_check: clinvar_20230508.vcf.gz.md5
+        file_index: clinvar_20230508.vcf.gz.tbi
+        outfile: grch38_clinvar_-20230508-.vcf.gz
+        outfile_check: grch38_clinvar_-20230508-.vcf.gz.md5
+        outfile_index: grch38_clinvar_-20230508-.vcf.gz.tbi
         outfile_check_method: md5sum
         url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
   dbnsfp:

From c77c281a3eed9ce03e88f62ef49e34d58157341b Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 16 May 2023 15:58:51 +0200
Subject: [PATCH 27/29] updating version

---
 CHANGELOG.md                      | 2 +-
 lib/MIP/Constants.pm              | 2 +-
 templates/mip_install_config.yaml | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8a7b5c892..6ec1d88ef 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## [Develop]
+## [12.0.0]
 
 - Set overlap requirement for merging two SVs to 0.8, down from the 0.95 default
 - Set overlap requirement for SV annotation to 0.6, up from 0.5
diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
index d6434afa0..9052437c5 100644
--- a/lib/MIP/Constants.pm
+++ b/lib/MIP/Constants.pm
@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{12.0.0-develop};
+Readonly our $MIP_VERSION => q{12.0.0};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index 23ccd8918..3881b1187 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -125,7 +125,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:develop
+    uri: docker.io/clinicalgenomics/mip:12.0.0
   multiqc:
     executable:
       multiqc:

From 6bc663a934d862a963a67a83a3866bac5f865419 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 16 May 2023 16:01:46 +0200
Subject: [PATCH 28/29] adding missing v in version

---
 templates/mip_install_config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index 3881b1187..26515fba8 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -125,7 +125,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:12.0.0
+    uri: docker.io/clinicalgenomics/mip:v12.0.0
   multiqc:
     executable:
       multiqc:

From 2b958acc6fa1b638942ab05f30b917618e55db3a Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 27 Jun 2023 13:31:37 +0200
Subject: [PATCH 29/29] add vcfanno config to download list

---
 templates/mip_download_rd_dna_config_-1.0-.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml
index 9adeef3d6..394a70101 100644
--- a/templates/mip_download_rd_dna_config_-1.0-.yaml
+++ b/templates/mip_download_rd_dna_config_-1.0-.yaml
@@ -131,8 +131,8 @@ reference:
     - 200520
   vcfanno_config:
     - v0.2
-    - v1.17
     - v1.18
+    - v1.19
   vcfanno_functions:
     - v1.0
 reference_feature: