module vcf2maf: Added working VEP cache with no annotations #563
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14 tasks
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Can you add it to the two Readmes:
I guess no way of somehow basing this on the existing fasta? |
It's based on the FASTA |
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perfect 🎉 |
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@FriederikeHanssen both README updated. |
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Apologies, my markdown formatter appears to have messed with the files. |
FriederikeHanssen
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Jun 20, 2022
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woops merged already 🤠 it'll be fine |
adamrtalbot
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Jun 20, 2022
Additions: - vcf2maf module created - If VEP is present in PATH, it is added to command - If VEP is missing, it is ignored (recommended to skip with --inhibit-vep) - VEP version automatically added to versions.yml - Uses VEP cache during testing which is added to test-datasets in nf-core/test-datasets#563 - Default Docker image includes VEP and vcf2maf - Test includes without VEP. Relates to nf-core#490
FriederikeHanssen
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Jun 20, 2022
vcf2maf module created Additions: - vcf2maf module created - If VEP is present in PATH, it is added to command - If VEP is missing, it is ignored (recommended to skip with --inhibit-vep) - VEP version automatically added to versions.yml - Uses VEP cache during testing which is added to test-datasets in nf-core/test-datasets#563 - Default Docker image includes VEP and vcf2maf - Test includes without VEP. Relates to #490
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Adds working minimal VEP cache for using with vcf2maf module (and possibly VEP module in future).
By including these two files, VEP runs correctly but doesn't annotate. I've reduced it to just chr22 to match the available test VCF and FASTA.