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Variable name change for var2vcf conversion arguments

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This commit is contained in:
Nicolas Vannieuwkerke 2022-04-28 16:38:49 +02:00
parent d626a1dcd3
commit 4b04ca22dd
2 changed files with 3 additions and 3 deletions
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4
modules/vardictjava/main.nf
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@ -21,7 +21,7 @@ process VARDICTJAVA {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def args_conversion = task.ext.args_conversion ?: '' def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
@ -35,7 +35,7 @@ process VARDICTJAVA {
$regions_of_interest \\ $regions_of_interest \\
| teststrandbias.R \\ | teststrandbias.R \\
| var2vcf_valid.pl \\ | var2vcf_valid.pl \\
$args_conversion \\ $args2 \\
-N $prefix \\ -N $prefix \\
| gzip -c > ${prefix}.vcf.gz | gzip -c > ${prefix}.vcf.gz

2
tests/modules/vardictjava/nextflow.config
View file

@ -4,6 +4,6 @@ process {
withName: VARDICTJAVA { withName: VARDICTJAVA {
ext.args = '' ext.args = ''
ext.args_conversion = '' ext.args2 = ''
} }
} }