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adjusted the bed variable name

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This commit is contained in:
Nicolas Vannieuwkerke 2022-05-09 15:51:19 +02:00
parent f6262b4a10
commit 1b63d03f8e
1 changed files with 2 additions and 2 deletions
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4
modules/rtgtools/vcfeval/main.nf
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@ -10,7 +10,7 @@ process RTGTOOLS_VCFEVAL {
input: input:
tuple val(meta), path(query_vcf), path(query_vcf_tbi) tuple val(meta), path(query_vcf), path(query_vcf_tbi)
tuple path(truth_vcf), path(truth_vcf_tbi) tuple path(truth_vcf), path(truth_vcf_tbi)
path(bed) path(truth_regions)
path(sdf) path(sdf)
output: output:
@ -23,7 +23,7 @@ process RTGTOOLS_VCFEVAL {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def regions = bed ? "--bed-regions=$bed" : "" def regions = truth_regions ? "--bed-regions=$truth_regions" : ""
def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf" def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf" def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"