diff --git a/conf/nanopore.config b/conf/nanopore.config index da8e2eed..830b9336 100644 --- a/conf/nanopore.config +++ b/conf/nanopore.config @@ -29,5 +29,9 @@ params { // Minimum coverage depth to call aa consequences of variant. csqDpThreshold = 20 - + + // medaka model used by artic minion + // {pore}_{device}_{caller variant}_{caller version} + medakaModel = 'r941_min_high_g351' + } diff --git a/environments/nanopore/environment.yml b/environments/nanopore/environment.yml index 32d40a3c..756816c4 100644 --- a/environments/nanopore/environment.yml +++ b/environments/nanopore/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - artic=1.1.3 + - artic=1.2.2 - pyyaml=5.3.1 diff --git a/modules/artic.nf b/modules/artic.nf index 2736c578..fd81972d 100644 --- a/modules/artic.nf +++ b/modules/artic.nf @@ -81,6 +81,7 @@ process articMinIONMedaka { """ artic minion --medaka \ ${minionFinalConfig} \ + --medaka-model ${params.medakaModel} \ --threads ${task.cpus} \ --scheme-directory ${schemeRepo} \ --read-file ${fastq} \