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Error: Panel index file requirement - Invalid filename format and missing file extension #21

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atrigila opened this issue Mar 24, 2024 · 1 comment · Fixed by #23
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@atrigila
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Description of the bug

The schema_input_panel.json required that the "panel index file cannot contain spaces and must have extension '.vcf' or '.bcf' with '.csi' or '.tbi' extension". However, 1000G index files, such as s3://1000genomes/release/20130502/ALL.chr20.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi
end with extension vcf.gz.tbi

Solution:

            "index": {
                "type": "string",
                "pattern": "^\\S+\\.(vcf|bcf)(\\.gz)?\\.(tbi|csi)$",
                "errorMessage": "Panel index file must be provided, cannot contain spaces and must have extension '.vcf' or '.bcf' with optional '.gz' extension and with '.csi' or '.tbi' extension"
            }

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@atrigila atrigila added the bug Something isn't working label Mar 24, 2024
@atrigila atrigila self-assigned this Mar 25, 2024
@LouisLeNezet
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That's effectively a mistake from me.
Are you working on it or do you want me to update it ?

@LouisLeNezet LouisLeNezet linked a pull request Mar 27, 2024 that will close this issue
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atrigila added a commit that referenced this issue Mar 27, 2024
Update schema_input_panel.json - Fix issue #21
atrigila added a commit that referenced this issue Mar 27, 2024
Update schema_input_panel.json - Fix issue #21
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2 participants