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fixed disabling of artic normalisation #258

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merged 1 commit into from
Sep 14, 2023
Merged

fixed disabling of artic normalisation #258

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8 changes: 4 additions & 4 deletions workflows/process/artic.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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 ${params.medaka_model} \
Expand Down Expand Up @@ -89,7 +89,7 @@ process artic_medaka_custom_bed {
tuple val(name), path("${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 ${normalise_threshold}" : '--normalise 0'
"""
# create a new primer dir as input for artic
mkdir -p primer_scheme/nCoV-2019
Expand Down Expand Up @@ -167,7 +167,7 @@ process artic_nanopolish {
tuple val(name), path("${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 \
${normalise_arg} \
Expand Down Expand Up @@ -234,7 +234,7 @@ process artic_nanopolish_custom_bed {
tuple val(name), path("${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
Expand Down