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Remove duplicated config-snippet for SENTIEON_GVCFTYPER #1548

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asp8200 opened this issue May 30, 2024 · 0 comments
Open

Remove duplicated config-snippet for SENTIEON_GVCFTYPER #1548

asp8200 opened this issue May 30, 2024 · 0 comments
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bug Something isn't working

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@asp8200
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asp8200 commented May 30, 2024

Description of the bug

Not much of a bug, but we have a duplicated config-snippet for SENTIEON_GVCFTYPER:

sarek/conf/modules/sentieon_dnascope_joint_germline.config

Lines 18 to 25 in f2852ff

// TO-DO: duplicate!!
withName: 'SENTIEON_GVCFTYPER' {
ext.args = { '--allow-old-rms-mapping-quality-annotation-data' }
ext.prefix = { meta.intervals_name }
publishDir = [
enabled: false
]
}

sarek/conf/modules/sentieon_haplotyper_joint_germline.config

Lines 18 to 24 in f2852ff

withName: 'SENTIEON_GVCFTYPER' {
ext.args = { '--allow-old-rms-mapping-quality-annotation-data' }
ext.prefix = { meta.intervals_name }
publishDir = [
enabled: false
]
}

Maxime and I figured that that config-snippet should be placed in conf/modules/sentieon.config. Anyways, it certainly should be duplicated.

https://nfcore.slack.com/archives/C05V9FRJYMV/p1717059187193919

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@asp8200 asp8200 added the bug Something isn't working label May 30, 2024
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@asp8200