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Master #2076

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9e67ba4
Merge pull request #2063 from Clinical-Genomics/release/12.0.3
jemten Dec 5, 2023
073b9e5
Merge pull request #2069 from Clinical-Genomics/release/12.1.0
jemten Mar 5, 2024
f08a9cd
adding dv report to deliverables
jemten Nov 11, 2025
ef91234
Merge pull request #2075 from Clinical-Genomics/release/12.1.1
jemten Nov 18, 2025
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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/).

## [12.1.1]

- Write Deepvariant report html file to deliverables

## [12.1.0]

- Adds optional trimming of reads with Fastp for the DNA workflow, turned on by default
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2 changes: 1 addition & 1 deletion lib/MIP/Constants.pm
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Expand Up @@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
);

## Set MIP version
Readonly our $MIP_VERSION => q{12.1.0};
Readonly our $MIP_VERSION => q{12.1.1};

## Cli
Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;
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14 changes: 12 additions & 2 deletions lib/MIP/Recipes/Analysis/Deepvariant.pm
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Expand Up @@ -16,7 +16,7 @@ use autodie qw{ :all };
use Readonly;

## MIPs lib/
use MIP::Constants qw{ $CONTAINER_MANAGER $EQUALS $LOG_NAME $NEWLINE $SPACE $UNDERSCORE };
use MIP::Constants qw{ $CONTAINER_MANAGER $DOT $EQUALS $LOG_NAME $NEWLINE $SPACE $UNDERSCORE };

BEGIN {

Expand Down Expand Up @@ -124,7 +124,7 @@ sub analysis_deepvariant {
use MIP::Program::Gnu::Bash qw{ gnu_export };
use MIP::Program::Deepvariant qw{ deepvariant };
use MIP::Recipe qw{ parse_recipe_prerequisites };
use MIP::Sample_info qw{ set_recipe_metafile_in_sample_info set_recipe_outfile_in_sample_info };
use MIP::Sample_info qw{ set_file_path_to_store set_recipe_metafile_in_sample_info set_recipe_outfile_in_sample_info };
use MIP::Script::Setup_script qw{ setup_script };

### PREPROCESSING:
Expand Down Expand Up @@ -239,6 +239,16 @@ sub analysis_deepvariant {
}
);

set_file_path_to_store(
{
format => q{meta},
id => $sample_id,
path => $outfile_path_prefix . $DOT . q{visual_report.html},
recipe_name => $recipe_name,
sample_info_href => $sample_info_href,
}
);

submit_recipe(
{
base_command => $profile_base_command,
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2 changes: 1 addition & 1 deletion templates/mip_install_config.yaml
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Expand Up @@ -129,7 +129,7 @@ container:
mip:
executable:
mip:
uri: docker.io/clinicalgenomics/mip:v12.1.0
uri: docker.io/clinicalgenomics/mip:v12.1.1
multiqc:
executable:
multiqc:
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