WIP: advisory for snpeff #3580
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| title: snpEff cache location change in pipelines using snpEff | ||||||||
| subtitle: All pipelines using snpEff are affected by the change of the default cache location in snpEff happening in August 2025. | ||||||||
| category: | ||||||||
| - pipelines | ||||||||
| - configuration | ||||||||
| type: incompatibility | ||||||||
| severity: high | ||||||||
| publishedDate: "2025-10-22" | ||||||||
| reporter: | ||||||||
| - maxulysse | ||||||||
| - | ||||||||
| reviewer: | ||||||||
| - maxulysse | ||||||||
| - | ||||||||
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| pipelines: | ||||||||
| - name: sarek | ||||||||
| versions: | ||||||||
| - 2.12.0 | ||||||||
| - name: rnavar | ||||||||
| versions: | ||||||||
| - 4.2.0 | ||||||||
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There was a problem hiding this comment. are these versions correct? |
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| modules: | ||||||||
| - name: snpeff_download | ||||||||
| - name: snpeff_snpeff | ||||||||
| subworkflows: | ||||||||
| - name: vcf_annotation_snpeff | ||||||||
| nextflowVersions: | ||||||||
| - ">=25.04.0 <25.04.3" | ||||||||
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There was a problem hiding this comment. i don't think this is dependent on Nextflow |
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| references: | ||||||||
| - title: snpeff issue regarding change of hosting location of cache and binaries | ||||||||
| description: Issues reporting the issue with snpeff download after the change of hosting location | ||||||||
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| url: https://github.com/pcingola/SnpEff/issues/602 | ||||||||
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| # Issue | ||||||||
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| https://github.com/pcingola/SnpEff/issues/602 | ||||||||
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There was a problem hiding this comment. not needed. will be added at the end
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| snpeff download is broken with older versions of sarek/rnavar due to changes in location for the storage of snpeff cache. | ||||||||
| snpeff download works with newer versions of sarek/rnavar with an updated of snpeff, but cache 105 is now not valid anymore (hopefully until a fix comes). | ||||||||
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| -> https://github.com/pcingola/SnpEff/issues/609 | ||||||||
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