diff --git a/workflows/process/artic.nf b/workflows/process/artic.nf index 42f6896..cba69a5 100755 --- a/workflows/process/artic.nf +++ b/workflows/process/artic.nf @@ -23,7 +23,7 @@ process artic_medaka { tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail script: - def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '' + def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '--normalise 0' """ artic minion --medaka \ --medaka-model ${params.medaka_model} \ @@ -89,7 +89,7 @@ process artic_medaka_custom_bed { tuple val(name), path("${name}.coverage_mask.txt"), emit: coverage_mask tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail script: - def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '' + def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '--normalise 0' """ # create a new primer dir as input for artic mkdir -p primer_scheme/nCoV-2019 @@ -167,7 +167,7 @@ process artic_nanopolish { tuple val(name), path("${name}.coverage_mask.txt"), emit: coverage_mask tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail script: - def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '' + def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '--normalise 0' """ artic minion --minimap2 \ ${normalise_arg} \ @@ -234,7 +234,7 @@ process artic_nanopolish_custom_bed { tuple val(name), path("${name}.coverage_mask.txt"), emit: coverage_mask tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail script: - def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '' + def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '--normalise 0' """ # create a new primer dir as input for artic mkdir -p primer_scheme/nCoV-2019