FEAT: Use annotation-cache and update VEP to v110 #1122
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| "use_annotation_cache_keys": { | ||
| "type": "boolean", | ||
| "fa_icon": "fas fa-toolbox", | ||
| "description": "Use annotation cache keys for snpeff_cache and vep_cache.", |
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can we get a help text with a bit more explanation
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like i am unsure now, if this referes to the new s3 bucket or if I want to define some cache locally or so
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yeah, basically that's because of how snpeff and vep store data, they're made for HPC, and I'm storing on cloud.
Plan would be to extrapolate that in the docs.
But I need to build a website for that.
| @@ -128,6 +128,10 @@ if (params.tools && (params.tools.split(',').contains('ascat') || params.tools.s | |||
| } | |||
| } | |||
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| if ((params.download_cache) && (params.snpeff_cache || params.vep_cache)) { | |||
| error("Please specify either `--download_cache` or `--snpeff_cache`, `--vep_cache`.\nhttps://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation") | |||
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did you update these docs already? Quick question how does this work for a cluster wide setup? I am thinking it would make sense to instruct users to predownload this, same as for igenomes and then supply the cache location (maybe sarek specific config specific config, to keep download costs low in terms of time and storage space for users)
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yeah, for a regular HPC, that depends if you build yourself or if you copy annotation_cache.
If you build locally, then no issue, just set up use_annotation_cache_keys to false.
If just basic mirror of annotation_cache then use_annotation_cache_keys should be set to true.
But for now, no other options.
FriederikeHanssen
requested changes
Jul 4, 2023
asp8200
reviewed
Jul 21, 2023
maxulysse
commented
Jul 21, 2023
asp8200
changed the title
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
FriederikeHanssen
approved these changes
Aug 17, 2023
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).